![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Last modified 13 months ago
#16079 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff848dd8dc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath (total: 120)
{"app_name":"ChimeraX","timestamp":"2024-10-07 11:01:13.00 +0100","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"C4E0BD6B-F7C7-42A1-8AA5-48A101C18E02"}
{
"uptime" : 280000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 12972,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-07 11:00:18.4754 +0100",
"codeSigningMonitor" : 0,
"incident" : "C4E0BD6B-F7C7-42A1-8AA5-48A101C18E02",
"pid" : 82842,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-04 14:02:04.8053 +0100",
"procStartAbsTime" : 247428069331916,
"procExitAbsTime" : 288279864277661,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5FC18D3C-1898-50CA-92F1-24E40C066179","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "22AFD314-FBF5-45F4-A151-6BB76F846F16",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 106,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "EA28EE74-4AB2-4A31-A088-6F9AB6CBCD0F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4381319168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10525a000-10525e000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":82842},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4381319168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10525a000-10525e000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[41,7,197,252,41,71,32,72,131,199,64,72,131,234,64,119,237,197,252,17,4,23,197,252,17,68,23,32,197,248,119,93,195,72,137,52,23,72,131,234,8,115,246,72,131,194,8,116,11,64,136,116,23,255,72,131,234,1,117,245,93,195,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,85,72,137,229,72,137,249,72,137,250,72,131,231,240,102,15,239,192,102,15,116,7,102,15,215,240,72,131,225,15,72,131,200,255,72,211,224,33,198,116,23,15,188,198,72,41,215,72,1,248,93,195,102,46,15,31,132,0,0,0,0,0,102,144,72,131,199,16,102,15,239,192,102,15,116,7,102,15,215,240,133,246,116,236,235,211,101,72,139,12,37,24,0,0,0,65,137,200,49,192,240,76,15,177,7,15,133,241,28,0,0,233,0,0],"offset":96}},"frames":[{"imageOffset":32182,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":216},{"imageOffset":24253,"symbol":"pthread_kill","symbolLocation":262,"imageIndex":217},{"imageOffset":282792,"symbol":"raise","symbolLocation":24,"imageIndex":218},{"imageOffset":2540852,"symbol":"faulthandler_fatal_error","symbolLocation":388,"imageIndex":214},{"imageOffset":16349,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":219},{"imageOffset":0,"imageIndex":220},{"imageOffset":38708055,"imageIndex":154},{"imageOffset":38399649,"imageIndex":154},{"imageOffset":36937448,"imageIndex":154},{"imageOffset":36958840,"imageIndex":154},{"imageOffset":108068521,"imageIndex":154},{"imageOffset":108093982,"imageIndex":154},{"imageOffset":82367923,"imageIndex":154},{"imageOffset":50359862,"imageIndex":154},{"imageOffset":50343563,"imageIndex":154},{"imageOffset":77361,"symbol":"displayConfigFinalizedProc","symbolLocation":253,"imageIndex":221},{"imageOffset":45844,"symbol":"CGSPostLocalNotification","symbolLocation":168,"imageIndex":221},{"imageOffset":44651,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":96,"imageIndex":221},{"imageOffset":3680956,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":206,"imageIndex":221},{"imageOffset":3680736,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":18,"imageIndex":221},{"imageOffset":6854,"symbol":"_dispatch_call_block_and_release","symbolLocation":12,"imageIndex":222},{"imageOffset":11708,"symbol":"_dispatch_client_callout","symbolLocation":8,"imageIndex":222},{"imageOffset":61919,"symbol":"_dispatch_main_queue_drain","symbolLocation":984,"imageIndex":222},{"imageOffset":60921,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":31,"imageIndex":222},{"imageOffset":769606,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":9,"imageIndex":223},{"imageOffset":503925,"symbol":"__CFRunLoopRun","symbolLocation":2459,"imageIndex":223},{"imageOffset":499986,"symbol":"CFRunLoopRunSpecific","symbolLocation":557,"imageIndex":223},{"imageOffset":190985,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":224},{"imageOffset":190486,"symbol":"ReceiveNextEventCommon","symbolLocation":665,"imageIndex":224},{"imageOffset":189793,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":66,"imageIndex":224},{"imageOffset":258417,"symbol":"_DPSNextEvent","symbolLocation":880,"imageIndex":225},{"imageOffset":9779952,"symbol":"-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1273,"imageIndex":225},{"imageOffset":198021,"symbol":"-[NSApplication run]","symbolLocation":603,"imageIndex":225},{"imageOffset":93965,"imageIndex":146},{"imageOffset":583190,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":171},{"imageOffset":545047,"symbol":"QCoreApplication::exec()","symbolLocation":119,"imageIndex":171},{"imageOffset":2261324,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":92,"imageIndex":164},{"imageOffset":1044954,"symbol":"cfunction_call","symbolLocation":90,"imageIndex":214},{"imageOffset":630769,"symbol":"_PyObject_MakeTpCall","symbolLocation":129,"imageIndex":214},{"imageOffset":1868407,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61255,"imageIndex":214},{"imageOffset":1802218,"symbol":"PyEval_EvalCode","symbolLocation":282,"imageIndex":214},{"imageOffset":1779827,"symbol":"builtin_exec","symbolLocation":483,"imageIndex":214},{"imageOffset":1047348,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":68,"imageIndex":214},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":214},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":214},{"imageOffset":2512477,"symbol":"pymain_run_module","symbolLocation":253,"imageIndex":214},{"imageOffset":2511137,"symbol":"Py_RunMain","symbolLocation":2225,"imageIndex":214},{"imageOffset":2515163,"symbol":"pymain_main","symbolLocation":43,"imageIndex":214},{"imageOffset":2515114,"symbol":"Py_Main","symbolLocation":42,"imageIndex":214},{"imageOffset":15770,"symbol":"main","symbolLocation":122,"imageIndex":215},{"imageOffset":25413,"symbol":"start","symbolLocation":1909,"imageIndex":226}],"id":4441339,"triggered":true,"threadState":{"r13":{"value":105553690284033},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":140704351096256,"symbolLocation":0,"symbol":"_main_thread"},"rsi":{"value":11},"r8":{"value":3},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":140704351096256,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":14757395258967641293},"r15":{"value":22},"rbx":{"value":11},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703221267894,"matchesCrashFrame":1},"rbp":{"value":140575580740112},"rsp":{"value":140575580740072},"r12":{"value":259},"rcx":{"value":140575580740072},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain"},{"id":4441655,"name":"ThreadPoolServiceThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140575730349312},"rsi":{"value":0},"r8":{"value":4},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553133371392},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145449823552},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703221279350},"rbp":{"value":123145449823536},"rsp":{"value":123145449823464},"r12":{"value":140575730349440},"rcx":{"value":123145449823464},"flavor":"x86_THREAD_STATE","rdi":{"value":11}},"frames":[{"imageOffset":43638,"symbol":"kevent64","symbolLocation":10,"imageIndex":216},{"imageOffset":75593716,"imageIndex":154},{"imageOffset":75593183,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75245773,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441656,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":200124001157120},"r9":{"value":200124001157120},"r15":{"value":200124001157120},"rbx":{"value":123145458224432},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145458223760},"rsp":{"value":123145458223656},"r12":{"value":33000},"rcx":{"value":123145458223656},"flavor":"x86_THREAD_STATE","rdi":{"value":123145458224432}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75297738,"imageIndex":154},{"imageOffset":75295997,"imageIndex":154},{"imageOffset":75295727,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441657,"name":"ThreadPoolBackgroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":268293722079232},"r9":{"value":268293722079232},"r15":{"value":268293722079232},"rbx":{"value":123145466625328},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145466624656},"rsp":{"value":123145466624552},"r12":{"value":33000},"rcx":{"value":123145466624552},"flavor":"x86_THREAD_STATE","rdi":{"value":123145466625328}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75297738,"imageIndex":154},{"imageOffset":75295853,"imageIndex":154},{"imageOffset":75295764,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441658,"name":"Chrome_IOThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140575742192384},"rsi":{"value":0},"r8":{"value":3},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553737123712},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145475026208},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703221279350},"rbp":{"value":123145475026192},"rsp":{"value":123145475026120},"r12":{"value":140575742192480},"rcx":{"value":123145475026120},"flavor":"x86_THREAD_STATE","rdi":{"value":12}},"frames":[{"imageOffset":43638,"symbol":"kevent64","symbolLocation":10,"imageIndex":216},{"imageOffset":75593716,"imageIndex":154},{"imageOffset":75593183,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":48358146,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441659,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":252900559290368},"r9":{"value":252900559290368},"r15":{"value":252900559290368},"rbx":{"value":123145483426880},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145483426208},"rsp":{"value":123145483426104},"r12":{"value":0},"rcx":{"value":123145483426104},"flavor":"x86_THREAD_STATE","rdi":{"value":123145483426880}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441665,"name":"Chrome_InProcGpuThread","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":223213745340416},"r9":{"value":223213745340416},"r15":{"value":223213745340416},"rbx":{"value":123145525431360},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145525430688},"rsp":{"value":123145525430584},"r12":{"value":0},"rcx":{"value":123145525430584},"flavor":"x86_THREAD_STATE","rdi":{"value":123145525431360}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441666,"name":"Chrome_ChildIOThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140575583645440},"rsi":{"value":0},"r8":{"value":1},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553161385568},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145533832480},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703221279350},"rbp":{"value":123145533832464},"rsp":{"value":123145533832392},"r12":{"value":140575583645504},"rcx":{"value":123145533832392},"flavor":"x86_THREAD_STATE","rdi":{"value":21}},"frames":[{"imageOffset":43638,"symbol":"kevent64","symbolLocation":10,"imageIndex":216},{"imageOffset":75593716,"imageIndex":154},{"imageOffset":75593183,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":122838530,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441667,"name":"CompositorTileWorker1","threadState":{"r13":{"value":2203318223616},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145542234112},"rsi":{"value":2203318223616},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":512},"r10":{"value":0},"r9":{"value":161},"r15":{"value":512},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145542233808},"rsp":{"value":123145542233656},"r12":{"value":0},"rcx":{"value":123145542233656},"flavor":"x86_THREAD_STATE","rdi":{"value":140575730429976}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":75462980,"imageIndex":154},{"imageOffset":113394117,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441668,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":234208861618176},"r9":{"value":234208861618176},"r15":{"value":234208861618176},"rbx":{"value":123145550634288},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145550633616},"rsp":{"value":123145550633512},"r12":{"value":0},"rcx":{"value":123145550633512},"flavor":"x86_THREAD_STATE","rdi":{"value":123145550634288}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75296343,"imageIndex":154},{"imageOffset":75296045,"imageIndex":154},{"imageOffset":75295784,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441669,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":373846838345728},"r9":{"value":373846838345728},"r15":{"value":373846838345728},"rbx":{"value":123145559034944},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145559034272},"rsp":{"value":123145559034168},"r12":{"value":0},"rcx":{"value":123145559034168},"flavor":"x86_THREAD_STATE","rdi":{"value":123145559034944}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441670,"name":"VizCompositorThread","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":367249768579072},"r9":{"value":367249768579072},"r15":{"value":367249768579072},"rbx":{"value":123145567435856},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145567435184},"rsp":{"value":123145567435080},"r12":{"value":15},"rcx":{"value":123145567435080},"flavor":"x86_THREAD_STATE","rdi":{"value":123145567435856}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":74666082,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441671,"name":"NetworkService","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140575742933760},"rsi":{"value":0},"r8":{"value":2},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553117319680},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145575837024},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703221279350},"rbp":{"value":123145575837008},"rsp":{"value":123145575836936},"r12":{"value":140575742933776},"rcx":{"value":123145575836936},"flavor":"x86_THREAD_STATE","rdi":{"value":22}},"frames":[{"imageOffset":43638,"symbol":"kevent64","symbolLocation":10,"imageIndex":216},{"imageOffset":75593716,"imageIndex":154},{"imageOffset":75593183,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441672,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":297980536029184},"r9":{"value":297980536029184},"r15":{"value":297980536029184},"rbx":{"value":123145584237632},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145584236960},"rsp":{"value":123145584236856},"r12":{"value":0},"rcx":{"value":123145584236856},"flavor":"x86_THREAD_STATE","rdi":{"value":123145584237632}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441673,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":300179559284736},"r9":{"value":300179559284736},"r15":{"value":300179559284736},"rbx":{"value":123145592638768},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145592638096},"rsp":{"value":123145592637992},"r12":{"value":0},"rcx":{"value":123145592637992},"flavor":"x86_THREAD_STATE","rdi":{"value":123145592638768}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75297738,"imageIndex":154},{"imageOffset":75296093,"imageIndex":154},{"imageOffset":75295774,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4441698,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":377145373229056},"r9":{"value":377145373229056},"r15":{"value":377145373229056},"rbx":{"value":123145604258880},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145604258208},"rsp":{"value":123145604258104},"r12":{"value":0},"rcx":{"value":123145604258104},"flavor":"x86_THREAD_STATE","rdi":{"value":123145604258880}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4442081,"name":"com.apple.NSEventThread","threadState":{"r13":{"value":21592279046},"rax":{"value":268451845},"rflags":{"value":518},"cpu":{"value":0},"r14":{"value":2},"rsi":{"value":21592279046},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":8589934592},"r10":{"value":726824430600192},"r9":{"value":726824430600192},"r15":{"value":726824430600192},"rbx":{"value":123145441419360},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":518},"rip":{"value":140703221239950},"rbp":{"value":123145441419200},"rsp":{"value":123145441419096},"r12":{"value":4294967295},"rcx":{"value":123145441419096},"flavor":"x86_THREAD_STATE","rdi":{"value":123145441419360}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":508357,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":143,"imageIndex":223},{"imageOffset":502837,"symbol":"__CFRunLoopRun","symbolLocation":1371,"imageIndex":223},{"imageOffset":499986,"symbol":"CFRunLoopRunSpecific","symbolLocation":557,"imageIndex":223},{"imageOffset":1692316,"symbol":"_NSEventThread","symbolLocation":122,"imageIndex":225},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4442090,"name":"MemoryInfra","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":705899349934080},"r9":{"value":705899349934080},"r15":{"value":705899349934080},"rbx":{"value":123145647508544},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145647507872},"rsp":{"value":123145647507768},"r12":{"value":0},"rcx":{"value":123145647507768},"flavor":"x86_THREAD_STATE","rdi":{"value":123145647508544}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75039155,"imageIndex":154},{"imageOffset":74666185,"imageIndex":154},{"imageOffset":75194449,"imageIndex":154},{"imageOffset":74879192,"imageIndex":154},{"imageOffset":75351720,"imageIndex":154},{"imageOffset":75352126,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4442091,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":706998861561856},"r9":{"value":706998861561856},"r15":{"value":706998861561856},"rbx":{"value":123145655909680},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145655909008},"rsp":{"value":123145655908904},"r12":{"value":0},"rcx":{"value":123145655908904},"flavor":"x86_THREAD_STATE","rdi":{"value":123145655909680}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75296343,"imageIndex":154},{"imageOffset":75295901,"imageIndex":154},{"imageOffset":75295804,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":4442626,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":18691697680640},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145438740480},"rsi":{"value":18691697680640},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4352},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4352},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145438740256},"rsp":{"value":123145438740104},"r12":{"value":0},"rcx":{"value":123145438740104},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442627,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":19791209308672},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145509167104},"rsi":{"value":19791209308672},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4608},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4608},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145509166880},"rsp":{"value":123145509166728},"r12":{"value":0},"rcx":{"value":123145509166728},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442628,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":21990232564736},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145509703680},"rsi":{"value":21990232564736},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5120},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5120},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145509703456},"rsp":{"value":123145509703304},"r12":{"value":0},"rcx":{"value":123145509703304},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442629,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":20890720936704},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145510240256},"rsi":{"value":20890720936704},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4864},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4864},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145510240032},"rsp":{"value":123145510239880},"r12":{"value":0},"rcx":{"value":123145510239880},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442630,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":23089744192768},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145510776832},"rsi":{"value":23089744192768},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5376},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5376},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145510776608},"rsp":{"value":123145510776456},"r12":{"value":0},"rcx":{"value":123145510776456},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442631,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":24189255820800},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145511313408},"rsi":{"value":24189255820800},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5632},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5632},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145511313184},"rsp":{"value":123145511313032},"r12":{"value":0},"rcx":{"value":123145511313032},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442632,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":25288767448832},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145511849984},"rsi":{"value":25288767448832},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5888},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5888},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145511849760},"rsp":{"value":123145511849608},"r12":{"value":0},"rcx":{"value":123145511849608},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442633,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":8796093028352},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145512386560},"rsi":{"value":8796093028352},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2048},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2048},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145512386336},"rsp":{"value":123145512386184},"r12":{"value":0},"rcx":{"value":123145512386184},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442634,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":9895604656384},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145512923136},"rsi":{"value":9895604656384},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2304},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2304},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145512922912},"rsp":{"value":123145512922760},"r12":{"value":0},"rcx":{"value":123145512922760},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442635,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":12094627912448},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145513459712},"rsi":{"value":12094627912448},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2816},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2816},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145513459488},"rsp":{"value":123145513459336},"r12":{"value":0},"rcx":{"value":123145513459336},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442636,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":10995116284416},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145513996288},"rsi":{"value":10995116284416},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2560},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2560},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145513996064},"rsp":{"value":123145513995912},"r12":{"value":0},"rcx":{"value":123145513995912},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442637,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":14293651168512},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145514532864},"rsi":{"value":14293651168512},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3328},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3328},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145514532640},"rsp":{"value":123145514532488},"r12":{"value":0},"rcx":{"value":123145514532488},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442638,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":13194139540480},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145515069440},"rsi":{"value":13194139540480},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3072},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3072},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145515069216},"rsp":{"value":123145515069064},"r12":{"value":0},"rcx":{"value":123145515069064},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442639,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":15393162796544},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145515606016},"rsi":{"value":15393162796544},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3584},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3584},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145515605792},"rsp":{"value":123145515605640},"r12":{"value":0},"rcx":{"value":123145515605640},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442640,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":17592186052608},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145516142592},"rsi":{"value":17592186052608},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4096},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4096},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145516142368},"rsp":{"value":123145516142216},"r12":{"value":0},"rcx":{"value":123145516142216},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":4442641,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":227},{"imageOffset":108261782,"imageIndex":154},{"imageOffset":108267659,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":16492674424576},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145516679168},"rsi":{"value":16492674424576},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3840},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3840},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145516678944},"rsp":{"value":123145516678792},"r12":{"value":0},"rcx":{"value":123145516678792},"flavor":"x86_THREAD_STATE","rdi":{"value":105553143847568}}},{"id":5317479,"name":"QFileInfoGatherer","threadState":{"r13":{"value":4402341479680},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145483964416},"rsi":{"value":4402341479680},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":1024},"r10":{"value":0},"r9":{"value":160},"r15":{"value":1024},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145483963968},"rsp":{"value":123145483963816},"r12":{"value":0},"rcx":{"value":123145483963816},"flavor":"x86_THREAD_STATE","rdi":{"value":105553595821888}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231675,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":4704546,"symbol":"QFileInfoGatherer::run()","symbolLocation":146,"imageIndex":166},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5318924,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":1103806595584},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145439277056},"rsi":{"value":1103806595584},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":256},"r10":{"value":0},"r9":{"value":160},"r15":{"value":256},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145439276912},"rsp":{"value":123145439276760},"r12":{"value":0},"rcx":{"value":123145439276760},"flavor":"x86_THREAD_STATE","rdi":{"value":4568406480,"symbolLocation":80,"symbol":"thread_status"}}},{"id":5318925,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":1103806595584},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145439813632},"rsi":{"value":1103806595584},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":256},"r10":{"value":0},"r9":{"value":160},"r15":{"value":256},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145439813488},"rsp":{"value":123145439813336},"r12":{"value":0},"rcx":{"value":123145439813336},"flavor":"x86_THREAD_STATE","rdi":{"value":4568406608,"symbolLocation":208,"symbol":"thread_status"}}},{"id":5318926,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145440350208},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145440350064},"rsp":{"value":123145440349912},"r12":{"value":0},"rcx":{"value":123145440349912},"flavor":"x86_THREAD_STATE","rdi":{"value":4568406736,"symbolLocation":336,"symbol":"thread_status"}}},{"id":5318927,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145440886784},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145440886640},"rsp":{"value":123145440886488},"r12":{"value":0},"rcx":{"value":123145440886488},"flavor":"x86_THREAD_STATE","rdi":{"value":4568406864,"symbolLocation":464,"symbol":"thread_status"}}},{"id":5318928,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145484500992},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145484500848},"rsp":{"value":123145484500696},"r12":{"value":0},"rcx":{"value":123145484500696},"flavor":"x86_THREAD_STATE","rdi":{"value":4568406992,"symbolLocation":592,"symbol":"thread_status"}}},{"id":5318929,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145502375936},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145502375792},"rsp":{"value":123145502375640},"r12":{"value":0},"rcx":{"value":123145502375640},"flavor":"x86_THREAD_STATE","rdi":{"value":4568407120,"symbolLocation":720,"symbol":"thread_status"}}},{"id":5318930,"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":194},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145502912512},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145502912368},"rsp":{"value":123145502912216},"r12":{"value":0},"rcx":{"value":123145502912216},"flavor":"x86_THREAD_STATE","rdi":{"value":4568407248,"symbolLocation":848,"symbol":"thread_status"}}},{"id":5326747,"threadState":{"r13":{"value":105553166653760},"rax":{"value":2420113409},"rflags":{"value":66050},"cpu":{"value":2},"r14":{"value":105553131685096},"rsi":{"value":105553128108032},"r8":{"value":0},"cr2":{"value":105553166651456},"rdx":{"value":65544},"r10":{"value":18437737153627684860},"r9":{"value":140704351111680,"symbolLocation":0,"symbol":"_dispatch_mgr_q"},"r15":{"value":65544},"rbx":{"value":105553166651456},"trap":{"value":14,"description":"(no mapping for user data read)"},"err":{"value":4},"r11":{"value":27021597764222976},"rip":{"value":140703219875023},"rbp":{"value":123145436055552},"rsp":{"value":123145436055536},"r12":{"value":105553597066752},"rcx":{"value":105553128108032},"flavor":"x86_THREAD_STATE","rdi":{"value":105553166651456}},"queue":"com.apple.CFMachPort","frames":[{"imageOffset":93391,"symbol":"_dispatch_source_handler_dispose","symbolLocation":9,"imageIndex":222},{"imageOffset":92047,"symbol":"_dispatch_source_cancel_callout","symbolLocation":77,"imageIndex":222},{"imageOffset":88992,"symbol":"_dispatch_source_invoke","symbolLocation":1199,"imageIndex":222},{"imageOffset":36194,"symbol":"_dispatch_lane_serial_drain","symbolLocation":387,"imageIndex":222},{"imageOffset":39319,"symbol":"_dispatch_lane_invoke","symbolLocation":377,"imageIndex":222},{"imageOffset":78868,"symbol":"_dispatch_root_queue_drain_deferred_wlh","symbolLocation":271,"imageIndex":222},{"imageOffset":77098,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":451,"imageIndex":222},{"imageOffset":11140,"symbol":"_pthread_wqthread","symbolLocation":327,"imageIndex":217},{"imageOffset":6863,"symbol":"start_wqthread","symbolLocation":15,"imageIndex":217}]},{"id":5327256,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":786301137715200},"r9":{"value":786301137715200},"r15":{"value":786301137715200},"rbx":{"value":123145492901168},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145492900496},"rsp":{"value":123145492900392},"r12":{"value":33000},"rcx":{"value":123145492900392},"flavor":"x86_THREAD_STATE","rdi":{"value":123145492901168}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75297738,"imageIndex":154},{"imageOffset":75295997,"imageIndex":154},{"imageOffset":75295727,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327727,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":731291196588032},"r9":{"value":731291196588032},"r15":{"value":731291196588032},"rbx":{"value":123145501302064},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703221239950},"rbp":{"value":123145501301392},"rsp":{"value":123145501301288},"r12":{"value":33000},"rcx":{"value":123145501301288},"flavor":"x86_THREAD_STATE","rdi":{"value":123145501302064}},"frames":[{"imageOffset":4238,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":216},{"imageOffset":63608,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":216},{"imageOffset":33144,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":216},{"imageOffset":4989,"symbol":"mach_msg","symbolLocation":19,"imageIndex":216},{"imageOffset":75634614,"imageIndex":154},{"imageOffset":75039302,"imageIndex":154},{"imageOffset":75293834,"imageIndex":154},{"imageOffset":75296343,"imageIndex":154},{"imageOffset":75295997,"imageIndex":154},{"imageOffset":75295727,"imageIndex":154},{"imageOffset":75466040,"imageIndex":154},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327926,"name":"Thread (pooled)","threadState":{"r13":{"value":152836411264000},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145434984448},"rsi":{"value":152836411264000},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":35584},"r10":{"value":0},"r9":{"value":160},"r15":{"value":35584},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145434984000},"rsp":{"value":123145434983848},"r12":{"value":999998000},"rcx":{"value":123145434983848},"flavor":"x86_THREAD_STATE","rdi":{"value":105553128115392}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231844,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":2209261,"imageIndex":171},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327928,"name":"Thread (pooled)","threadState":{"r13":{"value":112154481026816},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145436594176},"rsi":{"value":112154481026816},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":26112},"r10":{"value":0},"r9":{"value":160},"r15":{"value":26112},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145436593728},"rsp":{"value":123145436593576},"r12":{"value":999999000},"rcx":{"value":123145436593576},"flavor":"x86_THREAD_STATE","rdi":{"value":105553128764480}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231844,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":2209261,"imageIndex":171},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327929,"name":"Thread (pooled)","threadState":{"r13":{"value":112154481026816},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145437667328},"rsi":{"value":112154481026816},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":26112},"r10":{"value":0},"r9":{"value":160},"r15":{"value":26112},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145437666880},"rsp":{"value":123145437666728},"r12":{"value":999998000},"rcx":{"value":123145437666728},"flavor":"x86_THREAD_STATE","rdi":{"value":105553127986624}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231844,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":2209261,"imageIndex":171},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327937,"frames":[{"imageOffset":6848,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":0},"rsi":{"value":199443},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145501315072},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":0},"rbx":{"value":123145501839360},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703221484224},"rbp":{"value":0},"rsp":{"value":123145501839360},"r12":{"value":0},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145501839360}}},{"id":5327939,"name":"Thread (pooled)","threadState":{"r13":{"value":135244225215488},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145503449088},"rsi":{"value":135244225215488},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":31488},"r10":{"value":0},"r9":{"value":160},"r15":{"value":31488},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145503448640},"rsp":{"value":123145503448488},"r12":{"value":999998000},"rcx":{"value":123145503448488},"flavor":"x86_THREAD_STATE","rdi":{"value":105553127987392}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231844,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":2209261,"imageIndex":171},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]},{"id":5327940,"name":"Thread (pooled)","threadState":{"r13":{"value":145139829867776},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145503985664},"rsi":{"value":145139829867776},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":33536},"r10":{"value":0},"r9":{"value":160},"r15":{"value":33536},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703221251130},"rbp":{"value":123145503985216},"rsp":{"value":123145503985064},"r12":{"value":999995000},"rcx":{"value":123145503985064},"flavor":"x86_THREAD_STATE","rdi":{"value":105553128682560}},"frames":[{"imageOffset":15418,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":216},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":217},{"imageOffset":2231844,"imageIndex":171},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":171},{"imageOffset":2209261,"imageIndex":171},{"imageOffset":2191737,"imageIndex":171},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":217},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":217}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "x86_64",
"base" : 5679382528,
"size" : 32768,
"uuid" : "4cafbf15-47c9-3e93-abf0-7f8f01ea6b1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5658079232,
"size" : 49152,
"uuid" : "a9d30c5d-d3aa-3add-81c1-8d192b60c73b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so",
"name" : "_direct.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5668384768,
"size" : 704512,
"uuid" : "099ad96a-d10f-3f36-ad50-de62100b4a29",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so",
"name" : "_rotation.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5659406336,
"size" : 425984,
"uuid" : "c7fc9a60-2940-3dda-bf1c-e24d687981fd",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_pybind.cpython-311-darwin.so",
"name" : "_distance_pybind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5656829952,
"size" : 65536,
"uuid" : "ee0c90a6-01f4-3e5e-bf07-3e758786822f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ellip_harm_2.cpython-311-darwin.so",
"name" : "_ellip_harm_2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5615628288,
"size" : 32768,
"uuid" : "2d2e18f9-d234-3cac-81ed-447d252c8fa6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_comb.cpython-311-darwin.so",
"name" : "_comb.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5657817088,
"size" : 196608,
"uuid" : "33219854-ddbb-3fc0-a3b3-76c6c6fccf4f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_specfun.cpython-311-darwin.so",
"name" : "_specfun.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5658251264,
"size" : 147456,
"uuid" : "46274cdf-cee2-31ad-842f-7357cf9c6043",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_cdflib.cpython-311-darwin.so",
"name" : "_cdflib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5658849280,
"size" : 425984,
"uuid" : "5e6b8b45-5497-3e5f-9929-69523054da54",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs_cxx.cpython-311-darwin.so",
"name" : "_ufuncs_cxx.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5660086272,
"size" : 1048576,
"uuid" : "a744a694-8a95-3378-812e-5c646401936c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs.cpython-311-darwin.so",
"name" : "_ufuncs.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5656600576,
"size" : 147456,
"uuid" : "3978d5ae-2dd0-3b72-9bd7-9f867f5fa9d3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_hausdorff.cpython-311-darwin.so",
"name" : "_hausdorff.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5626441728,
"size" : 65536,
"uuid" : "52703c4a-be3c-3285-9786-1b1b36a2cf4d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_wrap.cpython-311-darwin.so",
"name" : "_distance_wrap.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5626212352,
"size" : 147456,
"uuid" : "7e2de6ef-0262-33f8-ac26-f9abcbd4436e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_voronoi.cpython-311-darwin.so",
"name" : "_voronoi.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5655502848,
"size" : 933888,
"uuid" : "ac10c62c-9202-3cc6-989f-4310464d04c3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_qhull.cpython-311-darwin.so",
"name" : "_qhull.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5656997888,
"size" : 638976,
"uuid" : "d83e1959-a587-3b0b-8304-c4a025a5c170",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_ckdtree.cpython-311-darwin.so",
"name" : "_ckdtree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5626626048,
"size" : 114688,
"uuid" : "baf13191-d471-3a9d-a557-38dcb64a6707",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_pava_pybind.cpython-311-darwin.so",
"name" : "_pava_pybind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5212966912,
"size" : 32768,
"uuid" : "8622832b-81a2-3d9c-af08-96517f62c486",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_lsap.cpython-311-darwin.so",
"name" : "_lsap.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5626847232,
"size" : 229376,
"uuid" : "7e5e7979-8cde-3a5e-badf-4535d1039d53",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_bglu_dense.cpython-311-darwin.so",
"name" : "_bglu_dense.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5655044096,
"size" : 327680,
"uuid" : "77846b2f-3c95-3f79-b410-e47ca8a614f7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_interpolative.cpython-311-darwin.so",
"name" : "_interpolative.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5206040576,
"size" : 32768,
"uuid" : "ad68821f-0af8-3485-b534-5aeb80a9d695",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_highs\/_highs_constants.cpython-311-darwin.so",
"name" : "_highs_constants.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5661990912,
"size" : 3096576,
"uuid" : "91a4359f-e233-3649-a058-2c2841384e51",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_highs\/_highs_wrapper.cpython-311-darwin.so",
"name" : "_highs_wrapper.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5141794816,
"size" : 16384,
"uuid" : "93be1d65-b07f-35c4-bb31-e1929c790d06",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_zeros.cpython-311-darwin.so",
"name" : "_zeros.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5625720832,
"size" : 131072,
"uuid" : "5f9dc654-1ca5-3130-9ab7-f68b87e78f9e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_lsq\/givens_elimination.cpython-311-darwin.so",
"name" : "givens_elimination.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5626097664,
"size" : 65536,
"uuid" : "c23bf3ac-e452-3b39-953d-bbe74bc5f5ee",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_minpack.cpython-311-darwin.so",
"name" : "_minpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5625982976,
"size" : 65536,
"uuid" : "7fc212d0-901c-3f3e-b4c8-769d176ba8bf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_slsqp.cpython-311-darwin.so",
"name" : "_slsqp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5624057856,
"size" : 81920,
"uuid" : "0287ae46-cb80-37e2-a35e-8452085d5ab4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_cobyla.cpython-311-darwin.so",
"name" : "_cobyla.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5625155584,
"size" : 114688,
"uuid" : "ae140cff-7ac0-3587-adf6-88443a9cd56f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_moduleTNC.cpython-311-darwin.so",
"name" : "_moduleTNC.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5623910400,
"size" : 98304,
"uuid" : "ec426f40-af2e-3651-ac5f-5ae3158d20e6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_lbfgsb.cpython-311-darwin.so",
"name" : "_lbfgsb.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5212086272,
"size" : 49152,
"uuid" : "2d8d0886-c73d-3ec7-9bf4-8a41535d058f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/_lib\/messagestream.cpython-311-darwin.so",
"name" : "messagestream.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5624827904,
"size" : 245760,
"uuid" : "856c7924-b6aa-3fa3-a34d-38fe27e13375",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_trlib\/_trlib.cpython-311-darwin.so",
"name" : "_trlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5615497216,
"size" : 65536,
"uuid" : "f805e6c8-a05f-379f-9ef1-5ba115744583",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_group_columns.cpython-311-darwin.so",
"name" : "_group_columns.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5208412160,
"size" : 49152,
"uuid" : "cca025d5-b375-3527-bb4f-f70cb9c8a77a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_minpack2.cpython-311-darwin.so",
"name" : "_minpack2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5625425920,
"size" : 212992,
"uuid" : "60c6fc77-0e71-30aa-a818-275c4e504cd5",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_reordering.cpython-311-darwin.so",
"name" : "_reordering.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5623566336,
"size" : 262144,
"uuid" : "ae50671a-77b8-392c-8a0e-25f8c3c0fd12",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_matching.cpython-311-darwin.so",
"name" : "_matching.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5624197120,
"size" : 245760,
"uuid" : "a094d70f-5141-3b7a-bc15-a94c1c2b0ae3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_flow.cpython-311-darwin.so",
"name" : "_flow.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5603573760,
"size" : 163840,
"uuid" : "0f5338a1-b354-3c81-bfbd-41e79c9095db",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_min_spanning_tree.cpython-311-darwin.so",
"name" : "_min_spanning_tree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5613776896,
"size" : 475136,
"uuid" : "c1f7970f-012c-3615-8866-19ce16d596a9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_traversal.cpython-311-darwin.so",
"name" : "_traversal.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5602799616,
"size" : 147456,
"uuid" : "32570ae1-c3d3-3465-9cb0-6adad8bd26fd",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_tools.cpython-311-darwin.so",
"name" : "_tools.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5604409344,
"size" : 393216,
"uuid" : "323215ff-ac89-3c17-a09a-3464580e925b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/csgraph\/_shortest_path.cpython-311-darwin.so",
"name" : "_shortest_path.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5615104000,
"size" : 98304,
"uuid" : "f73da7b7-ec7b-3739-8289-0832d1d1c2ea",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_propack\/_zpropack.cpython-311-darwin.so",
"name" : "_zpropack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5613481984,
"size" : 114688,
"uuid" : "fefe64af-ccbc-3fd5-b229-49f8b429db7f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_propack\/_cpropack.cpython-311-darwin.so",
"name" : "_cpropack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5601288192,
"size" : 81920,
"uuid" : "2ae3a9e4-22ca-3ebc-82d3-fd4e7518ef48",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_propack\/_dpropack.cpython-311-darwin.so",
"name" : "_dpropack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143121920,
"size" : 81920,
"uuid" : "0c8ee8a8-5442-3a6d-b022-d355293d0345",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_propack\/_spropack.cpython-311-darwin.so",
"name" : "_spropack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5604904960,
"size" : 409600,
"uuid" : "b7c2487c-aab9-39db-a489-2e8ee4ae336f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_eigen\/arpack\/_arpack.cpython-311-darwin.so",
"name" : "_arpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5613056000,
"size" : 344064,
"uuid" : "ba55f6eb-441d-360c-a733-e09129b78270",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/linalg\/_dsolve\/_superlu.cpython-311-darwin.so",
"name" : "_superlu.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5614366720,
"size" : 589824,
"uuid" : "115611d6-14c8-37e4-93f4-29abedf2f3aa",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/_csparsetools.cpython-311-darwin.so",
"name" : "_csparsetools.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5607796736,
"size" : 4669440,
"uuid" : "988cc771-7dfd-34ba-80a9-f1f64b028530",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/sparse\/_sparsetools.cpython-311-darwin.so",
"name" : "_sparsetools.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5604065280,
"size" : 262144,
"uuid" : "6125cc58-ac11-38cd-bad0-09b9e60c8cae",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_decomp_update.cpython-311-darwin.so",
"name" : "_decomp_update.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5602504704,
"size" : 196608,
"uuid" : "91d70e8a-91aa-3f9d-b08c-8546c203573d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/cython_blas.cpython-311-darwin.so",
"name" : "cython_blas.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5607305216,
"size" : 376832,
"uuid" : "3b2e1f8f-efb6-3e51-959d-f85ab702fc47",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_matfuncs_expm.cpython-311-darwin.so",
"name" : "_matfuncs_expm.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5603328000,
"size" : 163840,
"uuid" : "9ddab178-edc2-39d9-867c-558abd87e00a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_matfuncs_sqrtm_triu.cpython-311-darwin.so",
"name" : "_matfuncs_sqrtm_triu.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5603819520,
"size" : 163840,
"uuid" : "735115af-74c1-3d5e-a5b6-8e3d0a607f86",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_decomp_lu_cython.cpython-311-darwin.so",
"name" : "_decomp_lu_cython.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5603049472,
"size" : 196608,
"uuid" : "55e4a805-dcbd-3ae5-9c56-10879df6891f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_solve_toeplitz.cpython-311-darwin.so",
"name" : "_solve_toeplitz.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5601832960,
"size" : 442368,
"uuid" : "8cd8ce21-6b0b-3134-a92f-af9bf64be31b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/cython_lapack.cpython-311-darwin.so",
"name" : "cython_lapack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5600731136,
"size" : 458752,
"uuid" : "0a19c358-4a96-378b-9afd-3fd41169ab2e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_cythonized_array_utils.cpython-311-darwin.so",
"name" : "_cythonized_array_utils.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5605437440,
"size" : 1146880,
"uuid" : "0554d312-171f-38a2-a555-efbb381213ca",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_flapack.cpython-311-darwin.so",
"name" : "_flapack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5211480064,
"size" : 376832,
"uuid" : "41625c8f-94c5-3384-8533-6e1ea793bce8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_fblas.cpython-311-darwin.so",
"name" : "_fblas.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5875609600,
"size" : 66076672,
"uuid" : "40ef249b-28c0-36a0-a2c7-4f023a84cc12",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5615714304,
"size" : 6565888,
"uuid" : "ae37c55e-f850-3cf7-86e4-bbd86809bc1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libgfortran.5.dylib",
"name" : "libgfortran.5.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5601476608,
"size" : 319488,
"uuid" : "a1783d23-d187-3d92-ade7-2a80619e7485",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libquadmath.0.dylib",
"name" : "libquadmath.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142982656,
"size" : 69632,
"uuid" : "6d59656e-a224-3642-80b9-ca07ca06e7c1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libgcc_s.1.1.dylib",
"name" : "libgcc_s.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5211332608,
"size" : 81920,
"uuid" : "bd35c2ac-17ab-3c78-a864-41973c11f4db",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/_lib\/_ccallback_c.cpython-311-darwin.so",
"name" : "_ccallback_c.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5206360064,
"size" : 147456,
"uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5740294144,
"size" : 4210688,
"uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5145124864,
"size" : 16384,
"uuid" : "62001a43-deed-3f40-8d2d-57ad475e6c95",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5206261760,
"size" : 32768,
"uuid" : "cc4a7194-2678-3514-acc4-75a7275bf407",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5726769152,
"size" : 180224,
"uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5728772096,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5212213248,
"size" : 524288,
"uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5201928192,
"size" : 32768,
"uuid" : "3b76dfeb-802d-3ce8-9151-7ec4ff5a682b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5201747968,
"size" : 98304,
"uuid" : "ae16bb51-bedf-3c8a-9b96-5684b608789d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5202051072,
"size" : 49152,
"uuid" : "0e674aef-d74d-34e9-a46b-63ce1a6729b4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5203812352,
"size" : 49152,
"uuid" : "c84a9a90-56dd-385a-aad3-a15d44bc216b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5206626304,
"size" : 737280,
"uuid" : "85293474-c54e-32bd-967c-f9f9839646ae",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5202518016,
"size" : 131072,
"uuid" : "99497e49-7155-3c86-b62e-dd8a79f1be5d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5202255872,
"size" : 131072,
"uuid" : "272f9886-859c-3c84-8ea4-2bde196ca08b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5144829952,
"size" : 212992,
"uuid" : "9ff84874-4ecd-3fed-ba32-23b23bfaaecc",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5201600512,
"size" : 98304,
"uuid" : "3064d9b7-75d7-343e-bf98-036ded114223",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5137461248,
"size" : 32768,
"uuid" : "20c4af3a-4b84-3cc8-aa82-b08768c1116d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5137563648,
"size" : 65536,
"uuid" : "5cfe15a5-c7e4-36db-be9c-4d4ef3728796",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5127716864,
"size" : 16384,
"uuid" : "136e83be-523c-3e0a-8ee9-ac44338f577c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_mac_util.cpython-311-darwin.so",
"name" : "_mac_util.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 5126275072,
"size" : 53248,
"uuid" : "e554b85a-6614-3883-83d8-8eb3bd70a202",
"path" : "\/usr\/lib\/libobjc-trampolines.dylib",
"name" : "libobjc-trampolines.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5126488064,
"size" : 32768,
"uuid" : "eca278d3-d60a-39de-8179-e4e3d7044450",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacjp2.dylib",
"name" : "libqmacjp2.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5126066176,
"size" : 32768,
"uuid" : "52133b8a-b7f2-307f-99eb-74e22691cf79",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtga.dylib",
"name" : "libqtga.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5125967872,
"size" : 32768,
"uuid" : "0372cf7c-a608-3177-b1e1-bd312f0a6434",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqicns.dylib",
"name" : "libqicns.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5126176768,
"size" : 32768,
"uuid" : "cbbb200f-5258-33bb-baf8-e08d98ddc672",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqpdf.dylib",
"name" : "libqpdf.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5145219072,
"size" : 8765440,
"uuid" : "14ff39ad-fca1-3b61-ada4-f5f95bd02945",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPdf.framework\/Versions\/A\/QtPdf",
"name" : "QtPdf"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5123780608,
"size" : 32768,
"uuid" : "24897911-1bb1-3eb1-99c4-dc57d4440d49",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqsvg.dylib",
"name" : "libqsvg.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5124890624,
"size" : 245760,
"uuid" : "535f7dfd-d62a-33b3-9e52-af14094c4e5e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtSvg.framework\/Versions\/A\/QtSvg",
"name" : "QtSvg"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5126971392,
"size" : 442368,
"uuid" : "7a23c3a8-9cd7-3b95-9f4c-fe861273501d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtiff.dylib",
"name" : "libqtiff.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5124186112,
"size" : 622592,
"uuid" : "8fa53a40-5029-35c1-b403-de4b5ebc296b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqjpeg.dylib",
"name" : "libqjpeg.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5123682304,
"size" : 32768,
"uuid" : "587053e8-9ed2-37b5-bae3-52598b1c0ed9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacheif.dylib",
"name" : "libqmacheif.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5124087808,
"size" : 32768,
"uuid" : "6be87464-6bae-3acd-ba8a-0ad9c42d2192",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqico.dylib",
"name" : "libqico.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5125296128,
"size" : 589824,
"uuid" : "3b812afb-4558-3629-a105-54f0123a8756",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqwebp.dylib",
"name" : "libqwebp.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5123989504,
"size" : 32768,
"uuid" : "6665c7fa-5429-307c-ae72-f02b4663e991",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqwbmp.dylib",
"name" : "libqwbmp.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5123891200,
"size" : 32768,
"uuid" : "04424808-7083-3ca4-9997-8dae04f5e18a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqgif.dylib",
"name" : "libqgif.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5061578752,
"size" : 98304,
"uuid" : "7927d573-a75a-3483-b846-b34afb8cd28d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/vbo.cpython-311-darwin.so",
"name" : "vbo.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5040349184,
"size" : 32768,
"uuid" : "ada3a7a8-1026-3b4a-9d87-6fce8df2fb33",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/latebind.cpython-311-darwin.so",
"name" : "latebind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5049479168,
"size" : 32768,
"uuid" : "1936789e-b9b0-3e1f-8cfa-fc88f0803ad5",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/formathandler.cpython-311-darwin.so",
"name" : "formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5061218304,
"size" : 180224,
"uuid" : "d98e7117-18dd-37b7-9c74-472d0c79861a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/wrapper.cpython-311-darwin.so",
"name" : "wrapper.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5061869568,
"size" : 163840,
"uuid" : "84c28449-2886-395e-a902-73f67264df32",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/arraydatatype.cpython-311-darwin.so",
"name" : "arraydatatype.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5036023808,
"size" : 32768,
"uuid" : "2e49f12e-2bd1-36ff-a452-6af1ad840335",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/errorchecker.cpython-311-darwin.so",
"name" : "errorchecker.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5027246080,
"size" : 16384,
"uuid" : "5c82e5f4-7664-3325-95c1-a2286b531838",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb_lib\/_load_libs.cpython-311-darwin.so",
"name" : "_load_libs.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5031661568,
"size" : 32768,
"uuid" : "9c20a913-80f2-3790-82d6-f5f257f40a80",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb_lib\/lib\/libpdbconnect.dylib",
"name" : "libpdbconnect.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5049184256,
"size" : 180224,
"uuid" : "cd62d8e3-6428-319c-b174-d861a467788d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/surface\/_surface.cpython-311-darwin.so",
"name" : "_surface.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5049618432,
"size" : 163840,
"uuid" : "fe32f21a-cd3a-3ad4-9176-dddbd203789a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_image.cpython-311-darwin.so",
"name" : "_image.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5040103424,
"size" : 98304,
"uuid" : "b95403ec-ebee-307e-a234-a98fa49425bf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/kiwisolver\/_cext.cpython-311-darwin.so",
"name" : "_cext.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5049847808,
"size" : 671744,
"uuid" : "9f323cc7-da32-3fe1-b98b-163a8b0bc4f6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/ft2font.cpython-311-darwin.so",
"name" : "ft2font.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5035827200,
"size" : 131072,
"uuid" : "72e8fb51-e1eb-3955-ad6f-f9d432bd89fd",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_path.cpython-311-darwin.so",
"name" : "_path.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5025390592,
"size" : 16384,
"uuid" : "ab1ede05-8390-3ffd-92d7-7ce53a7c9be2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_c_internal_utils.cpython-311-darwin.so",
"name" : "_c_internal_utils.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5025325056,
"size" : 16384,
"uuid" : "e8200b4e-f282-3cd7-9be9-8f3798584047",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/termios.cpython-311-darwin.so",
"name" : "termios.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5038465024,
"size" : 393216,
"uuid" : "3d435819-60f1-382a-b0ff-03aa1fec22a9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imaging.cpython-311-darwin.so",
"name" : "_imaging.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5037301760,
"size" : 655360,
"uuid" : "de0a2e7d-b9a1-33f1-9bf1-e8db3a502cb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libtiff.6.dylib",
"name" : "libtiff.6.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5040451584,
"size" : 671744,
"uuid" : "5077f363-3598-3431-bc7b-2cfbf3a714d9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libjpeg.62.4.0.dylib",
"name" : "libjpeg.62.4.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5041205248,
"size" : 557056,
"uuid" : "5375f006-b7eb-3be7-88de-a910b38e7627",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libopenjp2.2.5.2.dylib",
"name" : "libopenjp2.2.5.2.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5024358400,
"size" : 131072,
"uuid" : "84f3a08c-6bf8-33d7-89c0-5e8026f4e202",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libz.1.3.1.dylib",
"name" : "libz.1.3.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5031383040,
"size" : 163840,
"uuid" : "5070a345-658e-31a4-80b9-d06f9abe9d5b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libxcb.1.dylib",
"name" : "libxcb.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5038071808,
"size" : 245760,
"uuid" : "2f03407e-0f9b-3146-b009-33e0f793869a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/liblzma.5.dylib",
"name" : "liblzma.5.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5025480704,
"size" : 16384,
"uuid" : "2b102593-309d-3ad2-98ff-fd87e42302d8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libXau.6.0.0.dylib",
"name" : "libXau.6.0.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5026852864,
"size" : 278528,
"uuid" : "6bf62b8d-952b-3c3e-87b6-67992b1c9e85",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_decimal.cpython-311-darwin.so",
"name" : "_decimal.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5018734592,
"size" : 16384,
"uuid" : "83a52d52-e452-3db7-8c1f-eee3d4bbc071",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_uuid.cpython-311-darwin.so",
"name" : "_uuid.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000753152,
"size" : 32768,
"uuid" : "b7700fae-a522-3c9e-81c7-8301374c2b6e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multibytecodec.cpython-311-darwin.so",
"name" : "_multibytecodec.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5036122112,
"size" : 1114112,
"uuid" : "0cfdf335-42fa-36ab-845a-44fda5a4f103",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/unicodedata.cpython-311-darwin.so",
"name" : "unicodedata.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5025062912,
"size" : 147456,
"uuid" : "d1f6d0b1-d05a-3cc7-8c15-0d72176e5bcb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/charset_normalizer\/md__mypyc.cpython-311-darwin.so",
"name" : "md__mypyc.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000450048,
"size" : 16384,
"uuid" : "143bfd0a-fbaa-3849-bbaa-9d3b2d44c38f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/charset_normalizer\/md.cpython-311-darwin.so",
"name" : "md.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5031813120,
"size" : 671744,
"uuid" : "99f6a3dc-9f85-3a3d-8ee5-4560b2308969",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/map\/_map.cpython-311-darwin.so",
"name" : "_map.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000081408,
"size" : 49152,
"uuid" : "f6ffe558-91c7-3148-a81a-e03bb00eac29",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cytmpl.cpython-311-darwin.so",
"name" : "cytmpl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5025558528,
"size" : 114688,
"uuid" : "60d71170-122f-3388-8946-9dc82b508714",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/tinyarray.cpython-311-darwin.so",
"name" : "tinyarray.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5023653888,
"size" : 458752,
"uuid" : "cd45a26e-b65b-3ce2-beb8-3b85f74e2cad",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cymol.cpython-311-darwin.so",
"name" : "cymol.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5024587776,
"size" : 212992,
"uuid" : "06f666f8-e01d-3977-8588-cd8763539de2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/libmolc.dylib",
"name" : "libmolc.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860637184,
"size" : 16384,
"uuid" : "d0ba4ed3-33c4-30c0-9fb8-0fcdd129cd4a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/_load_libs.cpython-311-darwin.so",
"name" : "_load_libs.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5027352576,
"size" : 1196032,
"uuid" : "61f0a987-8fa6-31d7-9915-0429ef9f504e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib",
"name" : "libatomstruct.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000335360,
"size" : 32768,
"uuid" : "d58debec-4cde-3edd-9365-e9ebb03fd2b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libelement.dylib",
"name" : "libelement.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000237056,
"size" : 16384,
"uuid" : "3edbdaff-bca7-3dde-878a-d25fb44e9018",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libpyinstance.dylib",
"name" : "libpyinstance.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860555264,
"size" : 32768,
"uuid" : "9b9ef339-f44c-3452-b5b0-92e4c1cfabb7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_csv.cpython-311-darwin.so",
"name" : "_csv.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860846080,
"size" : 16384,
"uuid" : "ed64b7f2-4c49-3dd2-ae71-a987d310a8d5",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/grp.cpython-311-darwin.so",
"name" : "grp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860780544,
"size" : 16384,
"uuid" : "82f64d2e-cca2-34b8-bb59-0743603ce84d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_scproxy.cpython-311-darwin.so",
"name" : "_scproxy.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5000540160,
"size" : 98304,
"uuid" : "65c5907a-9e69-3d89-a863-0f7df59fe19b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_ssl.cpython-311-darwin.so",
"name" : "_ssl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5018853376,
"size" : 393216,
"uuid" : "35eaab10-69c7-3234-bb9c-f3ec617bade8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/libssl.1.1.dylib",
"name" : "libssl.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860715008,
"size" : 16384,
"uuid" : "ab3e7bb1-b4dd-35a0-a44b-f87a59b1adbb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so",
"name" : "_queue.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4851740672,
"size" : 16384,
"uuid" : "1fceb320-1415-384c-914b-89deb7181eee",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_heapq.cpython-311-darwin.so",
"name" : "_heapq.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4852867072,
"size" : 49152,
"uuid" : "19fe4936-cd05-35cf-b67f-f07ddb83c195",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/array.cpython-311-darwin.so",
"name" : "array.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4852736000,
"size" : 65536,
"uuid" : "9b2e2c2e-1abb-329d-aeb2-9921c2085377",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_socket.cpython-311-darwin.so",
"name" : "_socket.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4852457472,
"size" : 180224,
"uuid" : "2eccca6e-b160-375e-979b-d1d174cf5497",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/pyexpat.cpython-311-darwin.so",
"name" : "pyexpat.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4853006336,
"size" : 163840,
"uuid" : "b955d9be-5646-38cb-aba8-4337ae17c16d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/styles\/libqmacstyle.dylib",
"name" : "libqmacstyle.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 5000863744,
"CFBundleShortVersionString" : "5.5.17",
"CFBundleIdentifier" : "com.apple.AMDRadeonX6000GLDriver",
"size" : 1376256,
"uuid" : "eb6aff55-6de7-3511-b4a8-1c584b1ec0fd",
"path" : "\/System\/Library\/Extensions\/AMDRadeonX6000GLDriver.bundle\/Contents\/MacOS\/AMDRadeonX6000GLDriver",
"name" : "AMDRadeonX6000GLDriver",
"CFBundleVersion" : "5.0.5"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4860915712,
"size" : 655360,
"uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4851834880,
"size" : 229376,
"uuid" : "e05fb3ee-5d42-3121-a19c-5ced50cb3132",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebEngineCore.abi3.so",
"name" : "QtWebEngineCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4419371008,
"size" : 32768,
"uuid" : "9d400ff9-e70a-351e-bb34-5259e39c88b8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebChannel.abi3.so",
"name" : "QtWebChannel.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4784033792,
"size" : 147456,
"uuid" : "34ad5a58-946c-3e72-bdbb-522e51148d3a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtPrintSupport.abi3.so",
"name" : "QtPrintSupport.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4848730112,
"size" : 475136,
"uuid" : "9513715b-6b36-3b31-8470-149dba6c1656",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtNetwork.abi3.so",
"name" : "QtNetwork.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4419485696,
"size" : 65536,
"uuid" : "e61f8860-5bfc-3097-919d-761e57850659",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebEngineWidgets.abi3.so",
"name" : "QtWebEngineWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4419141632,
"size" : 98304,
"uuid" : "c2859284-9c93-3dd9-a78b-839df778dfea",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineWidgets.framework\/Versions\/A\/QtWebEngineWidgets",
"name" : "QtWebEngineWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4501270528,
"size" : 294912,
"uuid" : "5154fa08-ddcc-3174-a42d-4e333e150ee9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPrintSupport.framework\/Versions\/A\/QtPrintSupport",
"name" : "QtPrintSupport"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5213057024,
"size" : 183599104,
"uuid" : "af091873-5278-3492-8e76-7c22e65c04ac",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4853338112,
"size" : 4210688,
"uuid" : "1b342485-b5a8-3134-8fbe-a4e607e770f3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQuick.framework\/Versions\/A\/QtQuick",
"name" : "QtQuick"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4842192896,
"size" : 425984,
"uuid" : "78a08e9f-03a8-3e55-b319-5d7390d883d3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGL.framework\/Versions\/A\/QtOpenGL",
"name" : "QtOpenGL"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4842831872,
"size" : 557056,
"uuid" : "17e7e0a2-1745-3a18-a3d2-87857777737e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQmlModels.framework\/Versions\/A\/QtQmlModels",
"name" : "QtQmlModels"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4779724800,
"size" : 180224,
"uuid" : "de6e3816-a208-301f-a7fc-0bbbb64c78a8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebChannel.framework\/Versions\/A\/QtWebChannel",
"name" : "QtWebChannel"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4843585536,
"size" : 4292608,
"uuid" : "33075afc-2a8b-3528-b0dd-4a5b769a2f54",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQml.framework\/Versions\/A\/QtQml",
"name" : "QtQml"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4834017280,
"size" : 1146880,
"uuid" : "b57854a4-c721-36b4-830e-2fe9e929a811",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtNetwork.framework\/Versions\/A\/QtNetwork",
"name" : "QtNetwork"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4849963008,
"size" : 458752,
"uuid" : "f7f96df9-e51a-3764-90a4-730a57198670",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPositioning.framework\/Versions\/A\/QtPositioning",
"name" : "QtPositioning"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4835524608,
"size" : 81920,
"uuid" : "a2d3acde-e0db-3d21-acc4-ebfa3db5fd5c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQuickWidgets.framework\/Versions\/A\/QtQuickWidgets",
"name" : "QtQuickWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4780756992,
"size" : 1523712,
"uuid" : "8cf677f1-f820-300f-bbea-491cfe548a9b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtGui.abi3.so",
"name" : "QtGui.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4772548608,
"size" : 2867200,
"uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4835786752,
"size" : 4931584,
"uuid" : "6b647ba7-e77f-36aa-937c-028f9cb4875c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4823351296,
"size" : 7274496,
"uuid" : "57e18c1d-e3ae-37c5-ada4-dcc62718794e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4780052480,
"size" : 540672,
"uuid" : "8b52e419-6929-39c7-8f25-239bd787b9b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtDBus.framework\/Versions\/A\/QtDBus",
"name" : "QtDBus"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4418945024,
"size" : 98304,
"uuid" : "3a35763b-1c12-3805-b15b-6ffa69bd1f52",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/sip.cpython-311-darwin.so",
"name" : "sip.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4418756608,
"CFBundleShortVersionString" : "3.0",
"CFBundleIdentifier" : "com.apple.security.csparser",
"size" : 94208,
"uuid" : "ba32b0db-6798-3ff5-9b01-a42fb9e96317",
"path" : "\/System\/Library\/Frameworks\/Security.framework\/Versions\/A\/PlugIns\/csparser.bundle\/Contents\/MacOS\/csparser",
"name" : "csparser",
"CFBundleVersion" : "61123.141.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4497551360,
"size" : 1720320,
"uuid" : "d186fce2-169a-3875-8ca4-f2fcd55371cf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4784517120,
"size" : 5373952,
"uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411473920,
"size" : 32768,
"uuid" : "b334e8fd-e63d-3cac-89e8-071a263d4818",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_json.cpython-311-darwin.so",
"name" : "_json.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4416413696,
"size" : 147456,
"uuid" : "2c719e3d-a419-3692-a578-2819f3d838f6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/geometry\/_geometry.cpython-311-darwin.so",
"name" : "_geometry.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411408384,
"size" : 16384,
"uuid" : "4161acf6-42c3-3364-aca8-8d14917132b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_opcode.cpython-311-darwin.so",
"name" : "_opcode.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4415512576,
"size" : 770048,
"uuid" : "15252f8d-5c11-35f9-8f3b-b8c1dd465de8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_generator.cpython-311-darwin.so",
"name" : "_generator.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4410855424,
"size" : 49152,
"uuid" : "9215cc4e-48d6-384f-aa4e-fa2ce81a8a1f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_sfc64.cpython-311-darwin.so",
"name" : "_sfc64.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411260928,
"size" : 81920,
"uuid" : "9e7a3d28-fb10-3335-bbe0-1f2a4e6e237a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_pcg64.cpython-311-darwin.so",
"name" : "_pcg64.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411707392,
"size" : 65536,
"uuid" : "b543ab2e-918d-3187-88cc-ed0733756a55",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_philox.cpython-311-darwin.so",
"name" : "_philox.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411559936,
"size" : 81920,
"uuid" : "5b3a56f1-c5e3-344a-86ff-810850013d80",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_mt19937.cpython-311-darwin.so",
"name" : "_mt19937.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4410413056,
"size" : 327680,
"uuid" : "05826eca-98c1-3b93-b72a-5c523819d49a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_bounded_integers.cpython-311-darwin.so",
"name" : "_bounded_integers.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4401614848,
"size" : 32768,
"uuid" : "1de3cb49-cee7-3aec-9885-69438bcbb671",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_blake2.cpython-311-darwin.so",
"name" : "_blake2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391456768,
"size" : 32768,
"uuid" : "c8a36b29-9fb1-3c9e-bb16-9698b6a379d4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_hashlib.cpython-311-darwin.so",
"name" : "_hashlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4493586432,
"size" : 2260992,
"uuid" : "9077f550-4289-3012-8803-cca73b9d943d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/libcrypto.1.1.dylib",
"name" : "libcrypto.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4410982400,
"size" : 196608,
"uuid" : "9de7ed17-62fe-3c59-a8e9-3d3074cb449e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_common.cpython-311-darwin.so",
"name" : "_common.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4401213440,
"size" : 163840,
"uuid" : "188f02a8-df66-3e0c-8946-153af5eaba44",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/bit_generator.cpython-311-darwin.so",
"name" : "bit_generator.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4411924480,
"size" : 655360,
"uuid" : "f65b5844-4c12-381e-8af8-637620272103",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/mtrand.cpython-311-darwin.so",
"name" : "mtrand.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4401483776,
"size" : 81920,
"uuid" : "2c97d6ef-aec3-361d-bc4d-0dd7137ad6ed",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/fft\/_pocketfft_internal.cpython-311-darwin.so",
"name" : "_pocketfft_internal.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4409135104,
"size" : 163840,
"uuid" : "95ecdafc-7133-362d-9f9c-dd26ff543a5b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/linalg\/_umath_linalg.cpython-311-darwin.so",
"name" : "_umath_linalg.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391276544,
"size" : 81920,
"uuid" : "cc072b20-11ee-3eb4-b287-8393ef51db95",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_ctypes.cpython-311-darwin.so",
"name" : "_ctypes.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391583744,
"size" : 81920,
"uuid" : "79cd772e-9106-339a-acb7-ba43552b15a7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/core\/_multiarray_tests.cpython-311-darwin.so",
"name" : "_multiarray_tests.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391038976,
"size" : 16384,
"uuid" : "6f069f98-51a6-3478-9053-9d1f2fbebd9b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_contextvars.cpython-311-darwin.so",
"name" : "_contextvars.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4390842368,
"size" : 114688,
"uuid" : "79de93b8-7f0e-3adc-8fde-969984151905",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_pickle.cpython-311-darwin.so",
"name" : "_pickle.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4393058304,
"size" : 4947968,
"uuid" : "fd4b95ff-f84a-34d3-939c-f932f374ddb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/core\/_multiarray_umath.cpython-311-darwin.so",
"name" : "_multiarray_umath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4501819392,
"size" : 66404352,
"uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4419674112,
"size" : 6565888,
"uuid" : "ae37c55e-f850-3cf7-86e4-bbd86809bc1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libgfortran.5.dylib",
"name" : "libgfortran.5.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4398759936,
"size" : 319488,
"uuid" : "a1783d23-d187-3d92-ade7-2a80619e7485",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libquadmath.0.dylib",
"name" : "libquadmath.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391137280,
"size" : 69632,
"uuid" : "6d59656e-a224-3642-80b9-ca07ca06e7c1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libgcc_s.1.1.dylib",
"name" : "libgcc_s.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388265984,
"size" : 16384,
"uuid" : "968f7d44-5fa3-31d9-8b22-92eb2206cc84",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/arrays\/_arrays.cpython-311-darwin.so",
"name" : "_arrays.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391747584,
"size" : 1130496,
"uuid" : "4442f722-a049-33ee-8cfe-e5e288b44421",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/arrays\/lib\/libarrays.dylib",
"name" : "libarrays.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388184064,
"size" : 32768,
"uuid" : "ce09d1ac-f6df-3770-9dda-8f52871a152d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so",
"name" : "select.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388343808,
"size" : 16384,
"uuid" : "8d17df9f-a171-32fe-848a-1380ca2546d4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_posixsubprocess.cpython-311-darwin.so",
"name" : "_posixsubprocess.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387606528,
"size" : 16384,
"uuid" : "1348d940-0f3a-37cb-9a27-37db7b4734d1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/fcntl.cpython-311-darwin.so",
"name" : "fcntl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387508224,
"size" : 32768,
"uuid" : "6333bf6e-f980-3714-b65f-a12997bfe10a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_struct.cpython-311-darwin.so",
"name" : "_struct.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388102144,
"size" : 32768,
"uuid" : "dc4ae342-b3c4-3716-a530-b1568a67f912",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/binascii.cpython-311-darwin.so",
"name" : "binascii.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388020224,
"size" : 32768,
"uuid" : "4e6494eb-704b-3e1a-9d97-751ef9b2d06a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387954688,
"size" : 16384,
"uuid" : "de8dfc82-ec28-378b-b945-07e7671a35b1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387889152,
"size" : 16384,
"uuid" : "cc52d89b-b174-3a9a-94ae-0c556ec7b21b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4388466688,
"size" : 196608,
"uuid" : "0fa75f51-66bf-3a60-a393-65ceea03012e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
"name" : "_lzma.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387823616,
"size" : 16384,
"uuid" : "4921b552-b90a-39c6-b791-14028366f5a0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4387725312,
"size" : 32768,
"uuid" : "6c0e3849-f845-3996-a69e-e956c62499ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4383838208,
"size" : 16384,
"uuid" : "52112d00-a676-3fba-b4d8-69e98fe5e2c3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4383690752,
"size" : 65536,
"uuid" : "ce1cdda7-c310-3834-8656-4829f8b0fa2a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4383944704,
"size" : 49152,
"uuid" : "c4d4107c-7508-3d61-88f1-4f1a33945090",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4401729536,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 4030464,
"uuid" : "514efc82-c424-3863-84a8-e24ffd50343d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4381319168,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703221235712,
"size" : 241656,
"uuid" : "54b50613-cc4b-3ace-a9ec-919ea83d5e5f",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703221477376,
"size" : 49144,
"uuid" : "d70de43a-2804-340a-804c-5d316c1e013b",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703220084736,
"size" : 557048,
"uuid" : "d7acdb03-4453-3d57-9b53-9f338bca635d",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703221678080,
"size" : 45048,
"uuid" : "4ea5bbf7-8ce1-37ab-916b-d14ffd7d2b4b",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703312564224,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4599807,
"uuid" : "9852f0e8-f530-3fe5-bf94-47d9a2266f87",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703219781632,
"size" : 290802,
"uuid" : "ffb968b0-807c-38bf-ae61-50a96c8d310c",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703221899264,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829181,
"uuid" : "c5e5acb6-9e44-3aa3-bd21-0a5b4a2eee5e",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2602"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703400595456,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732020,
"uuid" : "2aa738bf-9f72-3227-8bba-7eae7b9f080b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703279222784,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21172216,
"uuid" : "d0e19a37-f677-32b5-b3d2-005e60b90f7f",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.70.105"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703217758208,
"size" : 591904,
"uuid" : "18f658dd-20f3-324d-b7ac-8a9c60b574b3",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703220641792,
"size" : 503796,
"uuid" : "69eca28c-bfb7-35bf-ad4f-1bece712d239",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 140703217061888,
"size" : 25769803776,
"uuid" : "b8509d0f-c366-3716-9a03-efa00b40318a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=29.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=29.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nActivity Tracing 256K 1 \nCG image 452K 35 \nCG raster data 8K 1 \nColorSync 252K 31 \nCoreAnimation 2336K 148 \nCoreGraphics 16K 3 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreServices 720K 3 \nCoreUI image data 256K 2 \nFoundation 32K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 27.9G 4033 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_REALLOC (reserved) 8K 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 204K 51 \nStack 176.4M 52 \nStack Guard 56.0M 1 \nVM_ALLOCATE 913.6M 408 \nVM_ALLOCATE (reserved) 352.0M 3 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 47.9M 867 \n__DATA_CONST 65.6M 464 \n__DATA_DIRTY 1842K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 220.2M 218 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.1G 866 \ndyld private memory 40K 2 \nmapped file 261.5M 86 \nshared memory 2996K 29 \n=========== ======= ======= \nTOTAL 31.2G 7567 \nTOTAL, minus reserved VM space 30.9G 7567 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "fcc63f32cc2fe88f0f5d042cd2b2b7f5f6c50587",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c025b28b7f0e739e4fbe58",
"factorPackIds" : {
},
"deploymentId" : 240000019
},
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000015
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Fri Oct 4 13:17:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Wed Sep 25 19:02:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Tue Sep 24 13:00:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Mon Sep 16 15:36:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Wed Sep 11 12:56:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Mon Sep 9 04:24:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Fri Sep 6 19:48:00 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Log from Fri Sep 6 19:04:03 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.227, step 1, values float32
Log from Fri Sep 6 16:21:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
Log from Wed Sep 4 08:32:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Log from Wed Sep 4 05:32:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Log from Tue Sep 3 13:30:10 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
pixel 1.9, shown at level 0.362, step 2, values float32
Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
pixel 1.9, shown at level 0.34, step 1, values float32
Log from Tue Jul 30 11:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Log from Wed Jul 24 16:21:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Log from Thu Jul 18 19:11:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Log from Thu Jul 18 17:16:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Log from Thu Jul 11 13:31:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.359, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Log from Fri Jun 21 11:35:11 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Log from Tue Jun 11 16:35:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
Log from Mon Jun 3 09:50:12 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class001.mrc
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.0106, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class002.mrc
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class003.mrc
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.0124, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class004.mrc
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.0133, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class005.mrc
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class006.mrc
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class001.mrc
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class002.mrc
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.0105, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class003.mrc
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class004.mrc
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class005.mrc
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.0142, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class006.mrc
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.0149, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class001.mrc
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.0144, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class002.mrc
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class003.mrc
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class004.mrc
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class005.mrc
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.0143, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class006.mrc
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> volume all step 1
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job417_run_class001.mrc
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.0163, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job423.mrc
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.0162, step 2, values float32
> hide #!19 models
> volume #19 step 1
> volume #20 step 1
> hide #!20 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.362, step 2, values float32
> volume #21 step 1
> volume #21 level 0.4566
> volume #21 level 0.421
> volume #21 level 0.4151
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!15 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!15 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!7 models
> show #!9 models
> volume #7 level 0.01497
> volume #9 level 0.01231
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!12 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class001.mrc
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class002.mrc
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.0139, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class003.mrc
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class004.mrc
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class005.mrc
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class006.mrc
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.0181, step 2, values float32
> hide #!7 models
> hide #!9 models
> hide #!11 models
> hide #!12 models
> volume all step 1
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> volume #22 level 0.01345
> volume #22 level 0.0119
> volume #23 level 0.01121
> volume #24 level 0.01399
> volume #24 level 0.01119
> volume #24 level 0.01287
> volume #25 level 0.01349
> hide #!25 models
> show #!26 models
> volume #26 level 0.01133
> hide #!26 models
> show #!27 models
> volume #27 level 0.01296
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> volume #4 level 0.01157
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class001.mrc
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class002.mrc
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class003.mrc
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.0194, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class004.mrc
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class001.mrc
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class002.mrc
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class003.mrc
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class004.mrc
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.0189, step 2, values float32
> volume all step 1
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> volume #28 level 0.01275
> volume #28 level 0.01205
> volume #28 level 0.01231
> volume #29 level 0.01315
> volume #29 level 0.013
> volume #30 level 0.01741
> volume #31 level 0.01451
> volume #31 level 0.01487
> volume #32 level 0.01315
> volume #33 level 0.01302
> volume #34 level 0.01352
> volume #35 level 0.01616
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class001.mrc
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class002.mrc
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.0162, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class003.mrc
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class001.mrc
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class002.mrc
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.0162, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class003.mrc
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.0152, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class004.mrc
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.0168, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class005.mrc
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class001.mrc
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class002.mrc
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.0187, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class003.mrc
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class004.mrc
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.016, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class005.mrc
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class006.mrc
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> volume all step 1
> hide #!49 models
> hide #!48 models
> hide #!47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #!42 models
> hide #!41 models
> hide #!40 models
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> show #!37 models
> show #!38 models
> volume #36 level 0.013
> volume #37 level 0.013
> volume #38 level 0.013
> volume #39 level 0.013
> volume #40 level 0.013
> hide #!40 models
> show #!41 models
> volume #41 level 0.013
> show #!40 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!42 models
> volume #42 level 0.013
> hide #!42 models
> show #!43 models
> volume #43 level 0.013
> volume #43 level 0.012
> volume #44 level 0.013
> volume #45 level 0.013
> volume #46 level 0.013
> volume #47 level 0.013
> volume #48 level 0.013
> volume #49 level 0.013
> show #!44 models
> hide #!49 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> hide #!48 models
> show #!49 models
> hide #!49 models
> show #!48 models
> hide #!48 models
> hide #!44 models
> show #!43 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!43 models
> hide #!42 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!38 models
> hide #!38 models
> hide #!39 models
> show #!49 models
> hide #!49 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class001.mrc
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class002.mrc
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class003.mrc
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.0189, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class001.mrc
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.0193, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class002.mrc
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class003.mrc
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> hide #!51 models
> hide #!52 models
> hide #!53 models
> hide #!54 models
> hide #!55 models
> volume #50 level 0.013
> show #!51 models
> volume #51 level 0.013
> volume all level 0.013
> hide #!51 models
> hide #!50 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!50 models
> show #!51 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!51 models
> hide #!50 models
> hide #!52 models
> show #!51 models
> show #!50 models
> hide #!51 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> volume #50 level 0.012
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> ui tool show "Fit in Map"
> fitmap #50 inMap #15
Fit map Cl3D_job542_run_it025_class001.mrc in map
Cl3D_job411_run_it025_class003.mrc using 342972 points
correlation = 0.9888, correlation about mean = 0.813, overlap = 133.4
steps = 68, shift = 1.95, angle = 0.993 degrees
Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
Cl3D_job411_run_it025_class003.mrc (#15) coordinates:
Matrix rotation and translation
0.99987080 0.01439337 0.00715694 -5.19984751
-0.01434662 0.99987569 -0.00654060 6.68005810
-0.00725019 0.00643707 0.99995300 -1.28059948
Axis 0.37432567 0.41555671 -0.82897100
Axis point 407.25464445 414.10389399 0.00000000
Rotation angle (degrees) 0.99325686
Shift along axis 1.89108642
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!54 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> volume #54 level 0.012
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> fitmap #50 inMap #54
Fit map Cl3D_job542_run_it025_class001.mrc in map
Cl3D_job545_run_it025_class002.mrc using 342972 points
correlation = 0.9989, correlation about mean = 0.9796, overlap = 133
steps = 56, shift = 2.3, angle = 1.62 degrees
Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
Cl3D_job545_run_it025_class002.mrc (#54) coordinates:
Matrix rotation and translation
0.99982077 -0.01310087 0.01366700 -0.20479433
0.01319269 0.99989086 -0.00664955 -1.77455886
-0.01357839 0.00682866 0.99988449 1.74879695
Axis 0.33535327 0.67789597 0.65421345
Axis point 134.82260247 0.00000000 13.62266755
Rotation angle (degrees) 1.15146770
Shift along axis -0.12755828
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> hide #!50 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class001.mrc
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class002.mrc
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class003.mrc
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0184, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class001.mrc
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class002.mrc
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class003.mrc
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class004.mrc
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> volume all level 0.013
> hide #!57 models
> hide #!58 models
> hide #!59 models
> hide #!60 models
> hide #!61 models
> hide #!62 models
> show #!57 models
> hide #!56 models
> show #!58 models
> hide #!57 models
> volume #58 level 0.01852
> hide #!58 models
> show #!57 models
> hide #!57 models
> show #!56 models
> volume #56 level 0.012
> hide #!56 models
> show #!59 models
> volume #59 level 0.012
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> show #!59 models
> hide #!59 models
> volume #62 level 0.012
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!61 models
> hide #!61 models
> show #!60 models
> hide #!60 models
> show #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class001.mrc
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class002.mrc
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class003.mrc
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class004.mrc
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 2, values float32
> volume all step 1
> hide #!66 models
> hide #!65 models
> hide #!64 models
> volume #63 level 0.013
> volume #64 level 0.013
> volume #63 level 0.012
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class001.mrc
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.0187, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class002.mrc
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class003.mrc
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> volume all step 1
> hide #!68 models
> hide #!69 models
> show #!68 models
> hide #!67 models
> show #!69 models
> hide #!68 models
> volume #69 level 0.013
> volume #68 level 0.013
> volume #67 level 0.013
> show #!67 models
> hide #!67 models
> show #!68 models
> hide #!68 models
> show #!69 models
> hide #!69 models
> show #!29 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> show #!29 models
> hide #!29 models
> hide #!31 models
> show #!28 models
> show #!29 models
> hide #!29 models
> hide #!28 models
> show #!50 models
> hide #!50 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!50 models
> show #!51 models
> hide #!50 models
> hide #!51 models
> show #!53 models
> hide #!53 models
> show #!54 models
> show #!55 models
> hide #!55 models
> hide #!54 models
> show #!50 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> hide #!50 models
> show #!56 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class001.mrc
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class002.mrc
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class003.mrc
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class004.mrc
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class005.mrc
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0165, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class006.mrc
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> hide #!56 models
> volume all step 1
> hide #!71 models
> hide #!72 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> volume #70 level 0.013
> volume #71 level 0.013
> volume #71 level 0.01
> volume #71 level 0.012
> volume #72 level 0.013
> volume #72 level 0.01
> volume #72 level 0.012
> volume #73 level 0.012
> volume #74 level 0.013
> volume #75 level 0.013
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class001.mrc
Opened Cl3D_j577_run_it025_class001.mrc as #76, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class002.mrc
Opened Cl3D_j577_run_it025_class002.mrc as #77, grid size 294,294,294, pixel
1.9, shown at level 0.0135, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class003.mrc
Opened Cl3D_j577_run_it025_class003.mrc as #78, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class004.mrc
Opened Cl3D_j577_run_it025_class004.mrc as #79, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class005.mrc
Opened Cl3D_j577_run_it025_class005.mrc as #80, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class006.mrc
Opened Cl3D_j577_run_it025_class006.mrc as #81, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 2, values float32
> volume all step 1
> hide #!77 models
> hide #!78 models
> hide #!79 models
> hide #!80 models
> hide #!81 models
> volume #76 level 0.013
> volume #77 level 0.013
> volume #78 level 0.013
> volume #79 level 0.013
> volume #80 level 0.007565
> volume #80 level 0.02
> volume #80 level 0.012
> volume #81 level 0.012
> volume #81 level 0.01
> volume #81 level 0.008841
> volume #81 level 0.012
> volume #81 level 0.01
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!79 models
> hide #!79 models
> show #!78 models
> hide #!81 models
> hide #!78 models
> show #!77 models
> hide #!77 models
> show #!76 models
> hide #!76 models
> show #!81 models
> hide #!81 models
> show #!80 models
> hide #!80 models
> show #!79 models
> hide #!79 models
> show #!78 models
> hide #!78 models
> show #!77 models
> hide #!77 models
> show #!77 models
> hide #!77 models
> show #!76 models
> hide #!76 models
> show #!76 models
> hide #!76 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> show #!75 models
> hide #!75 models
> show #!74 models
> volume #74 level 0.01584
> volume #74 level 0.01357
> hide #!74 models
> show #!73 models
> hide #!73 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J577_class_02_00082_volume.mrc
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 0.888, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J583_class_02_00082_volume.mrc
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 0.827, step 1, values float32
> hide #!83 models
> volume #82 level 1.108
> volume #82 level 1.632
> volume #83 level 1.361
> open /Users/cvetkom/Downloads/cryosparc_P17_J610_002_volume_map.mrc
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.289, step 2, values float32
> volume #84 step 1
> volume #84 level 0.3974
> volume #84 level 0.3145
> volume #84 level 0.3879
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class001.mrc
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class002.mrc
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class003.mrc
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class004.mrc
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.0143, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class005.mrc
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class006.mrc
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.0179, step 2, values float32
> hide #!84 models
> volume all step 1
> hide #!86 models
> hide #!87 models
> hide #!88 models
> hide #!89 models
> hide #!90 models
> volume #85 level 0.013
> volume #86 level 0.013
> volume #86 level 0.012
> volume #87 level 0.012
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> volume #88 level 0.013
> volume #88 level 0.012
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> hide #!88 models
> show #!89 models
> show #!88 models
> hide #!88 models
> volume #89 level 0.013
> volume #90 level 0.013
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!89 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!84 models
> hide #!84 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class001.mrc
Opened Cl3D_j575_run_it025_class001.mrc as #91, grid size 294,294,294, pixel
1.9, shown at level 0.0167, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class002.mrc
Opened Cl3D_j575_run_it025_class002.mrc as #92, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class003.mrc
Opened Cl3D_j575_run_it025_class003.mrc as #93, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class004.mrc
Opened Cl3D_j575_run_it025_class004.mrc as #94, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class005.mrc
Opened Cl3D_j575_run_it025_class005.mrc as #95, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class006.mrc
Opened Cl3D_j575_run_it025_class006.mrc as #96, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> hide #!92 models
> hide #!93 models
> hide #!94 models
> hide #!95 models
> hide #!96 models
> volume all step 1
> volume #91 level 0.013
> volume #92 level 0.012
> volume #93 level 0.012
> volume #94 level 0.013
> volume #95 level 0.013
> close #91-96
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!88 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!88 models
> hide #!88 models
> show #!88 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> hide #!88 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!70 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!74 models
> hide #!74 models
> show #!73 models
> hide #!73 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!69 models
> hide #!69 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!32 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> hide #!41 models
> hide #!38 models
> show #!82 models
> show #!83 models
> hide #!83 models
> hide #!82 models
> show #!84 models
> hide #!84 models
> show #!82 models
> hide #!82 models
> show #!83 models
> hide #!83 models
> show #!84 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J611_002_volume_map.mrc
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.273, step 2, values float32
> hide #!84 models
> show #!84 models
> hide #!84 models
> volume #91 step 1
> show #!84 models
> volume #84 level 0.4
> volume #84 level 0.36
> hide #!91 models
> volume #91 level 0.36
> hide #!84 models
> show #!84 models
> hide #!84 models
> volume #91 level 0.4
> volume #91 level 0.45
> show #!84 models
> volume #84 level 0.45
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!90 models
> hide #!90 models
> show #!85 models
> show #!86 models
> hide #!86 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> hide #!86 models
> show #!28 models
> hide #!28 models
> show #!29 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #!29 models
> show #!29 models
> show #!28 models
> hide #!28 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> show #!28 models
> hide #!28 models
> hide #!31 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!28 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!28 models
> hide #!34 models
> show #!28 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!28 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!32 models
> show #!31 models
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!33 models
> hide #!34 models
> show #!35 models
> show #!32 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!36 models
> show #!37 models
> hide #!36 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!37 models
> show #!37 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!38 models
> hide #!37 models
> show #!39 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!41 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!41 models
> show #!43 models
> hide #!42 models
> hide #!43 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!44 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> hide #!48 models
> show #!49 models
> hide #!49 models
> show #!50 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!59 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> hide #!59 models
> show #!63 models
> show #!64 models
> show #!65 models
> hide #!65 models
> show #!66 models
> hide #!64 models
> hide #!63 models
> hide #!66 models
> show #!63 models
> show #!64 models
> hide #!63 models
> hide #!64 models
> show #!67 models
> hide #!67 models
> show #!68 models
> show #!69 models
> hide #!68 models
> show #!68 models
> hide #!69 models
> show #!69 models
> hide #!68 models
> hide #!69 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> hide #!70 models
> show #!75 models
> show #!74 models
> show #!73 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> show #!71 models
> hide #!71 models
> hide #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> show #!75 models
> hide #!74 models
> show #!74 models
> show #!73 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> show #!76 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> hide #!76 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!84 models
> hide #!84 models
> hide #!89 models
> show #!33 models
> show #!32 models
> hide #!32 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> hide #!38 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!70 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!76 models
> show #!75 models
> hide #!75 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> hide #!76 models
> show #!85 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!89 models
> show #!90 models
> hide #!90 models
> show #!32 models
> show #!34 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!15 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!15 models
> show #!50 models
> show #!51 models
> show #!52 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> hide #!50 models
> hide #!52 models
> show #!51 models
> hide #!51 models
> show #!50 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> show #!50 models
> hide #!50 models
> show #!51 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!51 models
> show #!51 models
> hide #!57 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> hide #!51 models
> show #!50 models
> show #!52 models
> hide #!52 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> show #!51 models
> hide #!50 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!54 models
> show #!50 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!57 models
> hide #!57 models
> show #!56 models
> hide #!56 models
> show #!56 models
> volume #56 level 0.013
> volume #56 level 0.012
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!56 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!56 models
> hide #!56 models
> show #!59 models
> hide #!59 models
> show #!56 models
> show #!50 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!50 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!59 models
> show #!60 models
> hide #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> show #!57 models
> hide #!57 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> show #!60 models
> hide #!59 models
> show #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> hide #!59 models
> show #!63 models
> hide #!63 models
> show #!2 models
> hide #!2 models
> show #!63 models
> show #!64 models
> hide #!63 models
> show #!65 models
> hide #!65 models
> show #!66 models
> hide #!64 models
> hide #!66 models
> show #!67 models
> hide #!67 models
> show #!68 models
> show #!69 models
> hide #!68 models
> hide #!69 models
> show #!70 models
> hide #!70 models
> show #!69 models
> hide #!69 models
> show #!68 models
> hide #!68 models
> show #!69 models
> show #!68 models
> hide #!68 models
> hide #!69 models
> show #!67 models
> show #!68 models
> hide #!67 models
> show #!69 models
> hide #!69 models
> show #!69 models
> hide #!68 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!69 models
> show #!69 models
> hide #!69 models
> show #!69 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> hide #!69 models
> show #!63 models
> show #!64 models
> hide #!63 models
> hide #!64 models
> show #!28 models
> show #!29 models
> hide #!28 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!29 models
> hide #!31 models
> show #!32 models
> show #!33 models
> show #!34 models
> show #!35 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!32 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!28 models
> hide #!28 models
> show #!29 models
> hide #!29 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!32 models
> show #!34 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!37 models
> show #!38 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #!37 models
> show #!38 models
> hide #!38 models
> show #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> hide #!36 models
> show #!36 models
> hide #!38 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!38 models
> hide #!32 models
> show #!39 models
> hide #!39 models
> show #!40 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> show #!42 models
> hide #!41 models
> show #!43 models
> hide #!42 models
> show #!42 models
> hide #!43 models
> show #!41 models
> hide #!42 models
> hide #!41 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!44 models
> show #!45 models
> hide #!44 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> show #!49 models
> hide #!48 models
> hide #!49 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!44 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> show #!49 models
> hide #!48 models
> hide #!49 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!44 models
> hide #!44 models
> show #!45 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!37 models
> hide #!37 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> show #!70 models
> show #!71 models
> hide #!70 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!75 models
> show #!70 models
> hide #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!74 models
> show #!72 models
> hide #!72 models
> show #!71 models
> show #!73 models
> hide #!73 models
> hide #!71 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> hide #!74 models
> hide #!70 models
> show #!76 models
> hide #!76 models
> show #!75 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!75 models
> show #!76 models
> show #!77 models
> hide #!76 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> close #76-81
> show #!85 models
> show #!86 models
> hide #!86 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!86 models
> hide #!87 models
> show #!88 models
> show #!89 models
> show #!85 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> hide #!85 models
> show #!85 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!89 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!89 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!90 models
> hide #!89 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!56 models
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!59 models
> hide #!56 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!56 models
> show #!59 models
> hide #!59 models
> hide #!56 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!35 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> hide #!35 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> show #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> hide #!87 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!85 models
> hide #!85 models
> show #!86 models
> show #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!87 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> show #!87 models
> hide #!86 models
> show #!86 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!86 models
> show #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!86 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!42 models
> hide #!42 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!43 models
> show #!41 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> hide #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> show #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> hide #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!41 models
> show #!42 models
> show #!43 models
> hide #!43 models
> hide #!42 models
> hide #!41 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!35 models
> show #!34 models
> hide #!35 models
> show #!35 models
> hide #!34 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!34 models
> hide #!34 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!91 models
> hide #!91 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J615_class_00_final_volume.mrc
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J616_class_00_final_volume.mrc
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.499, step 1, values float32
> volume #76 level 0.4164
> volume #77 level 0.4158
> volume #76 level 0.4
> volume #76 level 0.3
> volume #76 level 0.35
> volume #76 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J621_mask.mrc
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #78 level 1
> volume #78 color #cccc9980
> open /Users/cvetkom/Downloads/cryosparc_P17_J617_class_00_final_volume.mrc
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
> hide #!78 models
> hide #!79 models
> show #!79 models
> hide #!79 models
> show #!79 models
> hide #!76 models
> volume #79 level 0.3
> volume #79 level 0.4
> volume #79 level 0.35
> volume #79 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.339, step 2, values float32
> hide #!79 models
> volume #80 step 1
> volume #80 level 0.3095
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> hide #!81 models
> show #!81 models
> hide #!80 models
> volume #81 step 1
> show #!80 models
> hide #!80 models
> volume #81 level 0.35
> hide #!81 models
> show #!80 models
> volume #80 level 0.35
> volume #80 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J619_class_00_final_volume.mrc
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
> hide #!80 models
> show #!79 models
> hide #!79 models
> volume #92 level 0.35
> volume #92 level 0.4
> volume #92 level 0.4136
> show #!79 models
> hide #!92 models
> volume #79 level 0.3729
> show #!76 models
> hide #!79 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J623_007_volume_map.mrc
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.341, step 2, values float32
> hide #!76 models
> volume #93 step 1
> volume #93 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J626_class_01_00400_volume.mrc
Opened cryosparc_P17_J626_class_01_00400_volume.mrc as #94, grid size
128,128,128, pixel 4.36, shown at level 1.11, step 1, values float32
> hide #!93 models
> volume #94 level 0.8311
> close #94
> open /Users/cvetkom/Downloads/cryosparc_P17_J625_007_volume_map.mrc
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.341, step 2, values float32
> volume #94 step 1
> volume #94 level 0.3
> volume #94 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J631_class_01_00042_volume.mrc
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J629_class_01_00042_volume.mrc
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J628_class_01_00042_volume.mrc
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> hide #!94 models
> hide #!95 models
> hide #!96 models
> volume #97 level 1.082
> volume #97 level 1
> volume #96 level 1
> volume #95 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
Opened cryosparc_P17_J620_007_volume_map.mrc as #98, grid size 294,294,294,
pixel 1.9, shown at level 0.339, step 2, values float32
> close #98
> show #!80 models
> show #!93 models
Drag select of 80 cryosparc_P17_J620_007_volume_map.mrc , 93
cryosparc_P17_J623_007_volume_map.mrc
> select clear
> hide #!93 models
> show #!93 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> lighting soft
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!82 models
> hide #!82 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> hide #!93 models
> show #!81 models
> show #!80 models
> hide #!80 models
> volume #81 level 0.32
> volume #81 level 0.35
> show #!80 models
> select add #81
2 models selected
> ui mousemode right "rotate selected models"
> select subtract #81
Nothing selected
> hide #!81 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class006.mrc
Opened run_it025_class006.mrc as #98, grid size 294,294,294, pixel 1.9, shown
at level 0.0154, step 2, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class003.mrc
Opened run_it025_class003.mrc as #99, grid size 294,294,294, pixel 1.9, shown
at level 0.0157, step 2, values float32
> hide #!80 models
> hide #!98 models
> hide #!99 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class001.mrc
Opened run_it025_class001.mrc as #100, grid size 294,294,294, pixel 1.9, shown
at level 0.0158, step 2, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class002.mrc
Opened run_it025_class002.mrc as #101, grid size 294,294,294, pixel 1.9, shown
at level 0.0166, step 2, values float32
> hide #!101 models
> volume #98 step 1
> volume #99 step 1
> volume #100 step 1
> volume #101 step 1
> volume #100 level 0.01165
> volume #101 level 0.01425
> volume #101 level 0.01268
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!100 models
> show #!32 models
> volume #100 level 0.02
> hide #!32 models
> show #!32 models
> volume #100 level 0.015
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> volume #100 level 0.014
> volume #100 level 0.013
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> volume #101 level 0.014
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!101 models
> show #!99 models
> show #!98 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!88 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> close #98-101
> show #!97 models
> hide #!97 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.018, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class001.mrc
Opened Cl3D_j585_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class002.mrc
Opened Cl3D_j585_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class003.mrc
Opened Cl3D_j585_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class004.mrc
Opened Cl3D_j585_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class005.mrc
Opened Cl3D_j585_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.016, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class006.mrc
Opened Cl3D_j585_run_it025_class006.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.0002, step 2, values float32
> volume all step 1
> hide #!99 models
> hide #!100 models
> hide #!101 models
> hide #!102 models
> hide #!103 models
> hide #!104 models
> hide #!105 models
> hide #!106 models
> hide #!107 models
> hide #!108 models
> hide #!109 models
> hide #!110 models
> volume #98 level 0.013
> volume #98 level 0.012
> volume #99 level 0.012
> volume #100 level 0.013
> volume #101 level 0.012
> volume #102 level 0.012
> volume #103 level 0.013
> ui mousemode right zoom
> lighting simple
> show #!98 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> hide #!103 models
> show #!104 models
> show #!103 models
> hide #!104 models
> show #!104 models
> volume #104 level 0.013
> show #!103 models
> hide #!103 models
> volume #105 level 0.013
> volume #106 level 0.013
> volume #106 level 0.012
> volume #105 level 0.012
> volume #107 level 0.013
> volume #108 level 0.013
> volume #109 level 0.013
> volume #110 level -0.02134
> close #110
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class001.mrc
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class002.mrc
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.017, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class003.mrc
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class004.mrc
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class005.mrc
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.0127, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class006.mrc
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class007.mrc
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.0179, step 2, values float32
> close #105-109
> hide #!111 models
> hide #!112 models
> hide #!113 models
> hide #!114 models
> hide #!115 models
> hide #!116 models
> volume #110 level 0.012
> volume #111 level 0.012
> volume #111 level 0.013
> volume #110 step 1
> volume #111 step 1
> volume #112 step 1
> volume #112 level 0.013
> volume #113 step 1
> volume #113 level 0.012
> volume #114 step 1
> volume #114 level 0.012
> volume #115 step 1
> volume #115 level 0.013
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> volume #116 step 1
> volume #116 level 0.013
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> volume #111 level 0.01556
> volume #111 level 0.01455
> show #!110 models
> hide #!110 models
> hide #!111 models
> show #!111 models
> show #!99 models
> hide #!111 models
> show #!98 models
> hide #!99 models
> show #!110 models
> hide #!110 models
> hide #!98 models
> show #!110 models
> hide #!110 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class001.mrc
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class002.mrc
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class003.mrc
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class004.mrc
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class005.mrc
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class001.mrc
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class002.mrc
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class003.mrc
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class004.mrc
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class005.mrc
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
\u2014\u2014\u2014 End of log from Mon Jun 3 09:50:12 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!105 models
> show #!105 models
> show #!111 models
> hide #!111 models
> hide #!105 models
> show #!105 models
> hide #!105 models
> show #!105 models
> volume #105,106,107,108,109,117,118,119,120,121 level 0.013
> hide #!106 models
> show #!106 models
> hide #!109 models
> hide #!121 models
> hide #!120 models
> hide #!119 models
> hide #!118 models
> hide #!117 models
> hide #!108 models
> hide #!107 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!105 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!107 models
> hide #!107 models
> show #!108 models
> hide #!108 models
> show #!109 models
> hide #!109 models
> show #!108 models
> show #!109 models
> hide #!109 models
> show #!109 models
> hide #!109 models
> hide #!108 models
> show #!121 models
> hide #!121 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job325_0p95apix.mrc
Opened Ref3D_job325_0p95apix.mrc as #122, grid size 588,588,588, pixel 0.95,
shown at level 0.0107, step 4, values float32
> close #122
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!2 models
> volume #2 level 0.003218
> volume #2 level 0.006199
> volume #2 level 0.013
> hide #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
\u2014\u2014\u2014 End of log from Tue Jun 11 16:35:40 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!119 models
> hide #!119 models
> show #!120 models
> hide #!120 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class001.mrc
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.0174, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class002.mrc
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class003.mrc
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.0127, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class004.mrc
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class005.mrc
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class006.mrc
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class007.mrc
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.0175, step 2, values float32
> volume all step 1
> hide #!123 models
> hide #!124 models
> hide #!125 models
> hide #!126 models
> hide #!127 models
> hide #!128 models
> volume #122 level 0.01525
> volume #122 level 0.013
> volume #123 level 0.013
> show #!74 models
> volume #122 level 0.014
> volume #122 level 0.015
> hide #!74 models
> volume #124 level 0.013
> volume #125 level 0.013
> volume #126 level 0.013
> volume #127 level 0.013
> volume #128 level 0.014
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/run_it025_class001.mrc
Opened run_it025_class001.mrc as #129, grid size 294,294,294, pixel 1.9, shown
at level 0.0173, step 2, values float32
> close #129
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class001.mrc
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.0173, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class002.mrc
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class003.mrc
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class004.mrc
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class005.mrc
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class006.mrc
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class007.mrc
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.0169, step 2, values float32
> volume all step 1
> hide #!130 models
> hide #!131 models
> hide #!132 models
> hide #!133 models
> hide #!134 models
> hide #!135 models
> volume #129 level 0.015
> volume #129 level 0.014
> show #!130 models
> hide #!129 models
> volume #130 level 0.013
> volume #132 level 0.013
> volume #133 level 0.013
> volume #134 level 0.014
> volume #134 level 0.013
> volume #135 level 0.014
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> show #!133 models
> hide #!133 models
> hide #!135 models
> show #!134 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!135 models
> hide #!135 models
> show #!134 models
> hide #!134 models
> show #!133 models
> hide #!133 models
> show #!134 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!130 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class001.mrc
Opened Cl3D_j619_run_it025_class001.mrc as #136, grid size 320,320,320, pixel
1.9, shown at level 0.0108, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class002.mrc
Opened Cl3D_j619_run_it025_class002.mrc as #137, grid size 320,320,320, pixel
1.9, shown at level 0.00682, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class003.mrc
Opened Cl3D_j619_run_it025_class003.mrc as #138, grid size 320,320,320, pixel
1.9, shown at level 0.0091, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class004.mrc
Opened Cl3D_j619_run_it025_class004.mrc as #139, grid size 320,320,320, pixel
1.9, shown at level 0.0104, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class005.mrc
Opened Cl3D_j619_run_it025_class005.mrc as #140, grid size 320,320,320, pixel
1.9, shown at level 0.0128, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class006.mrc
Opened Cl3D_j619_run_it025_class006.mrc as #141, grid size 320,320,320, pixel
1.9, shown at level 0.013, step 2, values float32
> volume all step 1
> hide #!137 models
> hide #!138 models
> hide #!139 models
> hide #!140 models
> hide #!141 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!137 models
> hide #!137 models
> show #!136 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!137 models
> show #!138 models
> hide #!138 models
> show #!138 models
> hide #!137 models
> hide #!138 models
> show #!139 models
> hide #!139 models
> show #!140 models
> show #!141 models
> hide #!140 models
> hide #!141 models
> close #136-141
> show #!130 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> hide #!130 models
> show #!117 models
> show #!118 models
> hide #!118 models
> show #!118 models
> hide #!118 models
> show #!118 models
> hide #!117 models
> show #!117 models
> hide #!118 models
> show #!118 models
> hide #!117 models
> hide #!118 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> hide #!110 models
> show #!105 models
> show #!106 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!105 models
> show #!106 models
> hide #!105 models
> hide #!106 models
> show #!110 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> show #!122 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!110 models
> show #!99 models
> hide #!99 models
> show #!98 models
> volume #98 level 0.013
> hide #!130 models
> show #!130 models
> volume #99 level 0.013
> hide #!130 models
> show #!110 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> volume #110 level 0.013
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> hide #!110 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!129 models
> hide #!129 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J680_volume_map.mrc
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.413, step 2, values float32
> hide #!130 models
> volume #136 step 1
> volume #136 level 0.314
> open /Users/cvetkom/Downloads/cryosparc_P17_J676_class_00_final_volume.mrc
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.536, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J678_class_00_final_volume.mrc
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.529, step 1, values float32
> hide #!136 models
> hide #!138 models
> volume #137 level 0.5
> volume #137 level 0.4
> volume #137 level 0.3
> volume #138 level 0.3
> hide #!138 models
> show #!137 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J681_volume_map.mrc
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.411, step 2, values float32
> hide #!137 models
> volume #139 step 1
> volume #139 level 0.2939
> open /Users/cvetkom/Downloads/cryosparc_P17_J684_010_volume_map.mrc
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J685_007_volume_map.mrc
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.361, step 2, values float32
> hide #!139 models
> hide #!141 models
> volume #140 step 1
> volume #141 step 1
> volume #141 level 0.35
> volume #140 level 0.36
> volume #141 level 0.36
> open /Users/cvetkom/Downloads/cryosparc_P17_J677_class_00_final_volume.mrc
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.561, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J679_class_00_final_volume.mrc
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.55, step 1, values float32
> hide #!141 models
> hide #!143 models
> volume #142 level 0.3
> hide #!142 models
> show #!143 models
> volume #143 level 0.3
> volume #143 level 0.25
> volume #142 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J686_mask.mrc
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #144 level 1
> transparency #142.1#144.1 50
> transparency #142.1#144.1 0
> volume #144 color #cccc9980
> volume #142 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J688_007_volume_map.mrc
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J689_008_volume_map.mrc
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> hide #!142 models
> hide #!144 models
> hide #!146 models
> volume #145 step 1
> show #!146 models
> hide #!145 models
> volume #146 step 1
> show #!145 models
> hide #!145 models
> show #!145 models
> hide #!146 models
> show #!146 models
> hide #!145 models
> show #!145 models
> hide #!146 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J690_006_volume_map.mrc
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!145 models
> volume #147 step 1
> lighting soft
> show #!145 models
> hide #!147 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J691_008_volume_map.mrc
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J692_009_volume_map.mrc
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 2, values float32
> hide #!145 models
> hide #!149 models
> volume #148 step 1
> volume #149 step 1
> lighting soft
> lighting simple
> lighting soft
> show #!145 models
> hide #!149 models
> show #!146 models
> hide #!145 models
> hide #!146 models
> show #!145 models
> show #!148 models
> hide #!148 models
> show #!148 models
> show #!149 models
> hide #!149 models
> hide #!148 models
> show #!147 models
> hide #!147 models
> hide #!145 models
> show #!147 models
> hide #!147 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_map.mrc
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> volume #150 step 1
> show #!149 models
> hide #!149 models
> show #!149 models
> hide #!149 models
> show #!145 models
> hide #!150 models
> hide #!145 models
> show #!146 models
> hide #!146 models
> volume flip #145,146,148,149
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> hide #!154 models
> hide #!153 models
> hide #!152 models
> show #!150 models
> show #!152 models
> show #!153 models
> show #!154 models
> select add #150
2 models selected
> select add #151
4 models selected
> select add #152
6 models selected
> select add #153
8 models selected
> select add #154
10 models selected
> lighting simple
> select subtract #150
8 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #151,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#152,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#153,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#154,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87
> view matrix models
> #151,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#152,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#153,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#154,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38
> view matrix models
> #151,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#152,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#153,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#154,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58
> view matrix models
> #151,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#152,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#153,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#154,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2
> ui mousemode right "translate selected models"
> view matrix models
> #151,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#152,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#153,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#154,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84
> ui mousemode right "rotate selected models"
> view matrix models
> #151,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#152,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#153,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#154,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57
> ui mousemode right "translate selected models"
> view matrix models
> #151,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#152,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#153,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#154,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75
> select subtract #151
6 models selected
> select subtract #152
4 models selected
> select add #152
6 models selected
> select add #151
8 models selected
> select subtract #151
6 models selected
> select subtract #152
4 models selected
> select subtract #153
2 models selected
> select subtract #154
Nothing selected
> ui tool show "Fit in Map"
> fitmap #151 inMap #150
Fit map cryosparc_P17_J688_007_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 254273 points
correlation = 0.995, correlation about mean = 0.9397, overlap = 9.223e+04
steps = 100, shift = 5.99, angle = 2.29 degrees
Position of cryosparc_P17_J688_007_volume_map.mrc z flip (#151) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999140 -0.00359338 0.00207026 559.46992299
-0.00342330 0.99702499 0.07700290 -19.07074818
-0.00234080 0.07699515 -0.99702872 534.50211369
Axis -0.00175550 0.99925597 0.03852822
Axis point 280.01335285 0.00000000 267.30976851
Rotation angle (degrees) 179.87353804
Shift along axis 0.55470700
> fitmap #152 inMap #150
Fit map cryosparc_P17_J689_008_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 253853 points
correlation = 0.995, correlation about mean = 0.939, overlap = 9.217e+04
steps = 80, shift = 5.92, angle = 2.24 degrees
Position of cryosparc_P17_J689_008_volume_map.mrc z flip (#152) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999493 -0.00290598 0.00130357 559.46976174
-0.00279515 0.99693412 0.07819562 -19.59657377
-0.00152681 0.07819157 -0.99693718 533.82278737
Axis -0.00142641 0.99923323 0.03912681
Axis point 279.91004169 0.00000000 267.09682063
Rotation angle (degrees) 179.91885345
Shift along axis 0.50720275
> fitmap #153 inMap #150
Fit map cryosparc_P17_J691_008_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 254067 points
correlation = 0.9949, correlation about mean = 0.9379, overlap = 9.218e+04
steps = 100, shift = 5.99, angle = 2.29 degrees
Position of cryosparc_P17_J691_008_volume_map.mrc z flip (#153) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999153 -0.00354328 0.00209321 559.43919323
-0.00337135 0.99701735 0.07710412 -19.11074723
-0.00236017 0.07709641 -0.99702085 534.50415261
Axis -0.00172997 0.99925406 0.03857895
Axis point 280.00103027 0.00000000 267.30909738
Rotation angle (degrees) 179.87232473
Shift along axis 0.55630498
> fitmap #154 inMap #150
Fit map cryosparc_P17_J692_009_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 253930 points
correlation = 0.9949, correlation about mean = 0.9381, overlap = 9.218e+04
steps = 76, shift = 5.97, angle = 2.31 degrees
Position of cryosparc_P17_J692_009_volume_map.mrc z flip (#154) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999289 -0.00347463 0.00146599 559.52836319
-0.00335259 0.99707669 0.07633372 -18.91952628
-0.00172694 0.07632826 -0.99708125 534.48491699
Axis -0.00170809 0.99926890 0.03819344
Axis point 279.96163715 0.00000000 267.38037953
Rotation angle (degrees) 179.90846237
Shift along axis 0.55239822
> hide #!152 models
> hide #!153 models
> hide #!154 models
> volume #151 level 0.37
> ui mousemode right zoom
> lighting soft
> hide #!153 models
> show #!153 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!154 models
> hide #!154 models
> show #!153 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!150 models
> hide #!154 models
> show #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> hide #!32 models
> show #!32 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!32 models
> show #!32 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!32 models
> show #!130 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J699_class_00_00042_volume.mrc
Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
128,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
> hide #!75 models
> hide #!130 models
> volume #155 level 1.1
> volume #155 level 0.5
> volume #155 level 0.6
> volume #155 level 0.55
> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask.mrc
Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #156 level 1
> volume #156 color #ffffb27e
> volume #156 color #ffffb27d
> open /Users/cvetkom/Downloads/cryosparc_P17_J697_006_volume_map.mrc
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> hide #!155 models
> hide #!156 models
> volume #157 step 1
> volume #157 level 0.3
> volume #157 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask(1).mrc
Opened cryosparc_P17_J700_mask(1).mrc as #158, grid size 128,128,128, pixel
4.36, shown at level 1, step 1, values float32
> hide #!157 models
> show #!155 models
> show #!156 models
> hide #!156 models
> volume #158 color #b2b2ff7e
> volume #158 color #b2b2ff7d
> volume #158 level 1
> volume #155 level 0.8
> open /Users/cvetkom/Downloads/cryosparc_P17_J701_006_volume_map.mrc
Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J703_007_volume_map.mrc
Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!155 models
> hide #!158 models
> volume #159 step 1
> volume #160 step 1
> show #!159 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!157 models
> hide #!159 models
> show #!149 models
> hide #!149 models
> show #!149 models
> hide #!149 models
> show #!159 models
> show #!160 models
> select add #159
2 models selected
> select add #160
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #159,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73,#160,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73
> view matrix models
> #159,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69,#160,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69
> select subtract #159
2 models selected
> select subtract #160
Nothing selected
> hide #!159 models
> hide #!160 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!154 models
> hide #!154 models
> show #!159 models
> hide #!159 models
> hide #!157 models
> show #!159 models
> show #!160 models
> hide #!159 models
> hide #!160 models
> show #!157 models
> volume #157 level 0.36
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!157 models
> volume flip #157
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> hide #!159 models
> show #!159 models
> hide #!161 models
> show #!161 models
> select add #161
2 models selected
> view matrix models
> #161,0.76891,-0.22832,0.5972,-18.442,0.24486,-0.75768,-0.60494,582.05,0.59061,0.61138,-0.52668,39.302
> view matrix models
> #161,0.67534,0.22196,0.70331,-146.74,0.10898,-0.9732,0.20249,480.95,0.72941,-0.060102,-0.68143,229.96
> view matrix models
> #161,-0.93098,0.36002,0.06057,425.2,0.36288,0.89435,0.26166,-136.94,0.040032,0.26557,-0.96326,401.04
> view matrix models
> #161,-0.89701,0.43896,0.051772,395.36,0.44113,0.89642,0.042718,-105.12,-0.027658,0.061157,-0.99774,486.85
> select subtract #161
Nothing selected
> fitmap #161 inMap #159
Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
cryosparc_P17_J701_006_volume_map.mrc using 252025 points
correlation = 0.9982, correlation about mean = 0.9798, overlap = 9.355e+04
steps = 112, shift = 10, angle = 4.47 degrees
Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
cryosparc_P17_J701_006_volume_map.mrc (#159) coordinates:
Matrix rotation and translation
-0.99987255 -0.01520153 -0.00487783 564.75986128
0.01517723 -0.99987242 0.00497921 552.56953504
-0.00495290 0.00490455 0.99997571 0.88182116
Axis -0.00245783 0.00247107 0.99999393
Axis point 280.28257868 278.42842383 0.00000000
Rotation angle (degrees) 179.12967387
Shift along axis 0.85917190
> hide #!161 models
> show #!161 models
> hide #!159 models
> show #!159 models
> hide #!161 models
> show #!161 models
> hide #!159 models
> show #!159 models
> hide #!161 models
> hide #!159 models
> show #!155 models
> hide #!155 models
> show #!151 models
> volume #151 level 0.36
> ui mousemode right zoom
> show #!153 models
> show #!154 models
> hide #!153 models
> hide #!154 models
> hide #!151 models
> show #!151 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!151 models
> show #!150 models
> hide #!150 models
> show #!150 models
> volume #150 level 0.36
> hide #!81 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!81 models
> hide #!150 models
> show #!150 models
> show #!157 models
> hide #!157 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> show #!160 models
> select add #159
2 models selected
> select add #160
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #159,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66,#160,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66
> ui mousemode right "rotate selected models"
> view matrix models
> #159,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92,#160,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92
> select subtract #160
2 models selected
> select subtract #159
Nothing selected
> fitmap #159 inMap #150
Fit map cryosparc_P17_J701_006_volume_map.mrc in map
cryosparc_P17_J693_006_volume_map.mrc using 253555 points
correlation = 0.995, correlation about mean = 0.9467, overlap = 9.384e+04
steps = 92, shift = 15.9, angle = 4.91 degrees
Position of cryosparc_P17_J701_006_volume_map.mrc (#159) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
0.99990377 -0.01280700 0.00533263 1.75411257
-0.01349030 -0.98727395 0.15845557 514.15896836
0.00323543 -0.15851226 -0.98735171 596.92132464
Axis -0.99997579 0.00661630 -0.00215569
Axis point 0.00000000 280.88748875 277.95683594
Rotation angle (degrees) 170.88086929
Shift along axis 0.36097960
> fitmap #160 inMap #150
Fit map cryosparc_P17_J703_007_volume_map.mrc in map
cryosparc_P17_J693_006_volume_map.mrc using 254051 points
correlation = 0.9949, correlation about mean = 0.946, overlap = 9.382e+04
steps = 140, shift = 15.9, angle = 4.85 degrees
Position of cryosparc_P17_J703_007_volume_map.mrc (#160) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
0.99989095 -0.01388197 0.00503895 2.09422029
-0.01450557 -0.98723491 0.15860902 514.34229109
0.00277282 -0.15866482 -0.98732861 597.00803822
Axis -0.99997256 0.00714230 -0.00196544
Axis point 0.00000000 281.00771740 277.97254777
Rotation angle (degrees) 170.87196021
Shift along axis 0.40604025
> hide #!160 models
> hide #!159 models
> show #!159 models
> hide #!150 models
> show #!157 models
> hide #!157 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!160 models
> hide #!160 models
> show #!161 models
> hide #!161 models
> show #!159 models
> show #!161 models
> hide #!161 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!160 models
> hide #!159 models
> show #!159 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> hide #!160 models
> show #!159 models
> hide #!159 models
> show #!157 models
> show #!159 models
> hide #!159 models
> hide #!157 models
> show #!150 models
> show #!159 models
> hide #!159 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> show #!159 models
> hide #!150 models
> show #!150 models
> hide #!159 models
> hide #!150 models
> show #!151 models
> show #!150 models
> hide #!151 models
> show #!151 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> hide #!151 models
> show #!150 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_mask_refine.mrc
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 2, values float32
> volume #162 step 1
> volume #162 color #e5bf9980
> volume #162 level 1
> volume #162 color #e5bf9967
> volume #162 color #e5bf9966
> volume #150 level 0.3
> volume #150 level 0.2
> hide #!162 models
> show #!162 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J704_mask.mrc
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> hide #!162 models
> volume #163 step 1
> volume #163 color #99bfe565
> volume #163 color #99bfe566
> volume #163 level 1
> show #!162 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!162 models
> show #!162 models
> hide #!162 models
> show #!162 models
> hide #!162 models
> volume #163 level 0.5
> volume #163 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J707_009_volume_map.mrc
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> hide #!163 models
> hide #!150 models
> volume #164 step 1
> volume #164 level 0.384
> volume #164 level 0.35
> volume #164 level 0.3
> volume #164 level 0.2
> open /Users/cvetkom/Downloads/cryosparc_P17_J708_mask.mrc
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> hide #!164 models
> show #!164 models
> hide #!165 models
> show #!165 models
> volume #165 step 1
> volume #165 level 1
> volume #165 color #b2b2b27c
> volume #165 color #b2b2b26b
> volume #165 color #b2b2b263
> volume #165 color #b2b2b265
> volume #165 color #b2b2b266
> hide #!165 models
> volume #164 level 0.5
> volume #164 level 0.4
> open /Users/cvetkom/Downloads/cryosparc_P17_J705_006_volume_map.mrc
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.359, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J706_004_volume_map.mrc
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!164 models
> volume #166 step 1
> volume #167 step 1
> show #!164 models
> hide #!167 models
> show #!165 models
> hide #!165 models
> hide #!164 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J695_class_00_final_volume.mrc
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.544, step 1, values float32
> volume #168 level 0.3
> volume #168 level 0.25
> volume #168 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J714_mask.mrc
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #169 color #ffb2ff7d
> volume #169 color #ffb2ff67
> volume #169 color #ffb2ff66
> volume #169 level 1
> hide #!168 models
> show #!168 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask.mrc
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #170 color #ffb2b266
> volume #170 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask(1).mrc
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
> volume #171 color #b2ffb266
> volume #171 level 1
> show #!169 models
> hide #!171 models
> show #!171 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!170 models
> hide #!171 models
> show #!171 models
> hide #!171 models
> show #!171 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> hide #!168 models
> hide #!170 models
> hide #!171 models
> volume #172 step 1
> show #!168 models
> hide #!168 models
> show #!168 models
> hide #!168 models
> show #!164 models
> hide #!164 models
> show #!164 models
> hide #!172 models
> show #!172 models
> hide #!164 models
> volume #172 level 0.4
> volume #172 level 0.38
> volume #172 level 0.36
> open /Users/cvetkom/Downloads/cryosparc_P17_J710_008_volume_map.mrc
Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J712_007_volume_map.mrc
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.349, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J711_009_volume_map.mrc
Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
pixel 1.9, shown at level 0.353, step 2, values float32
> hide #!172 models
> hide #!174 models
> hide #!173 models
> show #!173 models
> hide #!175 models
> volume #173 step 1
> volume #174 step 1
> volume #175 step 1
> volume #173 level 0.3
> volume #173 level 0.2
> show #!164 models
> hide #!164 models
> show #!175 models
> volume #175 level 0.2
> hide #!175 models
> show #!175 models
> hide #!173 models
> show #!173 models
> hide #!175 models
> show #!175 models
> hide #!175 models
> volume #173 level 0.25
> volume #173 level 0.2
> volume #173 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> volume #176 step 1
> volume #176 color #ffffb266
> volume #176 level 1
> close #176
> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> volume #176 step 1
> volume #176 color #b2ffff66
> volume #176 level 1
> show #!174 models
> hide #!173 models
> hide #!176 models
> volume #174 level 0.2
> volume #174 level 0.25
> volume #174 level 0.2
> show #!173 models
> hide #!174 models
> show #!174 models
> hide #!173 models
> hide #!174 models
> show #!151 models
> show #!152 models
> show #!153 models
> show #!154 models
> hide #!154 models
> hide #!153 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!153 models
> hide #!151 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!152 models
> hide #!152 models
> hide #!153 models
> show #!152 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!153 models
> hide #!153 models
> show #!147 models
> hide #!151 models
> hide #!147 models
> show #!147 models
> show #!145 models
> hide #!145 models
> hide #!147 models
> show #!145 models
> hide #!145 models
> show #!175 models
> show #!174 models
> hide #!175 models
> hide #!174 models
> show #!167 models
> hide #!167 models
> show #!168 models
> hide #!168 models
> show #!167 models
> hide #!167 models
> show #!168 models
> hide #!168 models
> show #!166 models
> hide #!166 models
> show #!173 models
> show #!174 models
> hide #!174 models
> hide #!173 models
> show #!161 models
> hide #!161 models
> show #!160 models
> hide #!160 models
> show #!154 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> hide #!153 models
> show #!152 models
> show #!153 models
> hide #!153 models
> hide #!152 models
> show #!151 models
> hide #!151 models
> show #!150 models
> hide #!150 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
> ui mousemode right zoom
[Repeated 1 time(s)]
> show #!176 models
> hide #!176 models
> show #!175 models
> hide #!175 models
> show #!175 models
> hide #!175 models
> show #!174 models
> hide #!174 models
> show #!173 models
> hide #!173 models
> show #!172 models
> hide #!172 models
> show #!171 models
> hide #!171 models
> open 6SKL fromDatabase pdb format mmcif
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #177
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
Non-standard residues in 6skl #177
---
ANP \u2014 phosphoaminophosphonic acid-adenylate ester
MG \u2014 magnesium ion
ZN \u2014 zinc ion
> lighting simple
> select /2
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> select /6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select /4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select /5
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
\u2014\u2014\u2014 End of log from Fri Jun 21 11:35:11 2024 \u2014\u2014\u2014
opened ChimeraX session
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select subtract #177
Nothing selected
> hide #!177 models
> show #!174 models
> hide #!174 models
> show #!166 models
> show #!167 models
> hide #!166 models
> show #!166 models
> hide #!167 models
> show #!167 models
> hide #!166 models
> show #!166 models
> hide #!167 models
> hide #!166 models
> show #!166 models
> show #!172 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!172 models
> hide #!166 models
> show #!172 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
Opened cryosparc_P17_J721_006_volume_map.mrc as #158, grid size 294,294,294,
pixel 1.9, shown at level 0.346, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J719_007_volume_map.mrc
Opened cryosparc_P17_J719_007_volume_map.mrc as #178, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J717_007_volume_map.mrc
Opened cryosparc_P17_J717_007_volume_map.mrc as #179, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
> hide #!172 models
> show #!172 models
> hide #!172 models
> volume #179 step 1
> volume #178 step 1
> volume #178 level 0.4299
> volume #158 step 1
> close #158
> close #179
> close #178
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map_sharp.mrc
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.35, step 2, values float32
> volume #158 step 1
> volume #158 level 0.4035
> volume #158 level 0.3381
> show #!172 models
> show #!166 models
> hide #!172 models
> hide #!166 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #178 step 1
> volume #178 level 0.5544
> volume #178 level 0.3502
> close #178
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #178 step 1
> volume #178 level 0.9947
> volume #179 step 1
> volume #179 level 0.1617
> volume #179 level 0.152
> show #!172 models
> hide #!172 models
> lighting soft
> volume #179 level 0.1695
> hide #!179 models
> show #!172 models
> volume #172 level 0.3737
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!172 models
> volume #166 level 0.3843
> show #!172 models
> hide #!172 models
> show #!172 models
> hide #!172 models
> show #!172 models
> hide #!166 models
> hide #!172 models
> show #!178 models
> hide #!178 models
> show #!172 models
> volume #172 level 0.3509
> show #!171 models
> hide #!171 models
> hide #!172 models
> show #!179 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
Opened cryosparc_P17_J709_007_volume_map.mrc as #180, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> hide #!179 models
> hide #!180 models
> close #180
> open /Users/cvetkom/Downloads/cryosparc_P17_J787_004_volume_map_sharp.mrc
Opened cryosparc_P17_J787_004_volume_map_sharp.mrc as #180, grid size
588,588,588, pixel 0.95, shown at level 0.196, step 4, values float32
> volume #180 level 0.3198
> volume #180 step 1
> volume #180 level 0.4233
> volume #180 level 0.4003
> open /Users/cvetkom/Downloads/cryosparc_P17_J786_005_volume_map_sharp.mrc
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.204, step 4, values float32
> volume #181 step 1
> volume #181 level 0.3442
> volume #181 level 0.4
> open /Users/cvetkom/Downloads/cryosparc_P17_J787_005_volume_map_sharp.mrc
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.21, step 4, values float32
> hide #!181 models
> volume #182 step 1
> volume #182 level 0.3526
> volume #182 level 0.4
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job690/mask.mrc
Opened mask.mrc as #183, grid size 588,588,588, pixel 0.95, shown at level 1,
step 4, values float32
> close #183
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map_sharp.mrc
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.153, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_mask_fsc.mrc
Opened cryosparc_P17_J792_volume_mask_fsc.mrc as #184, grid size 520,520,520,
pixel 0.95, shown at level 5e-05, step 4, values float32
> hide #!182 models
> volume #183 step 1
> volume #183 level 0.3916
> lighting soft
> lighting full
> volume #184 step 1
> volume #184 level 1
> volume #184 color #b2b2ff80
> volume #184 level 0
> volume #184 level 0.03512
> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
Opened cryosparc_P17_J760_mask(1).mrc as #185, grid size 520,520,520, pixel
0.95, shown at level 5e-05, step 4, values float32
> volume #185 step 1
> volume #185 color #ffb2ff7f
> volume #185 level 1
[Repeated 1 time(s)]
> open /Users/cvetkom/Downloads/cryosparc_P17_J757_volume_map.mrc
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.0189, step 4, values float32
> volume #186 level 0.07565
> volume #186 step 1
> hide #!183 models
> hide #!185 models
> volume #186 level 0.1989
> volume #186 level 0.1509
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map.mrc
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.0388, step 4, values float32
> hide #!183 models
> hide #!186 models
> volume #187 level 0.0929
> volume #187 step 1
> volume #187 level 0.2473
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!186 models
> volume #186 level 0.1781
> hide #!186 models
> show #!186 models
> hide #!186 models
> show #!186 models
> volume #186 level 0.2261
> hide #!186 models
> show #!186 models
> hide #!186 models
> show #!184 models
> show #!185 models
> volume #184 level 1
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!183 models
> hide #!183 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map.mrc
Opened cryosparc_P17_J795_007_volume_map.mrc as #188, grid size 520,520,520,
pixel 0.95, shown at level 0.0131, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map_sharp.mrc
Opened cryosparc_P17_J795_007_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.0597, step 4, values float32
> hide #!184 models
> hide #!187 models
> volume #188 level 0.1056
> volume #188 step 1
> volume #188 level 0.2671
> volume #188 level 0.2362
> volume #189 level 0.3385
> volume #189 step 1
> close #188-189
> close #185
> close #184
> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map_sharp.mrc
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.213, step 4, values float32
> volume #184 level 0.4718
> volume #184 step 1
> volume #184 level 0.7484
> volume #184 level 0.846
> show #!183 models
> hide #!183 models
> show #!183 models
> hide #!183 models
> show #!183 models
> hide #!183 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map.mrc
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.0436, step 4, values float32
> hide #!185 models
> show #!185 models
> hide #!184 models
> volume #185 level 0.2092
> volume #185 step 1
> volume #185 level 0.2795
> lighting soft
> volume #185 level 0.2092
> volume #185 level 0.08268
> volume #185 level 0.1858
> volume #185 level 0.1904
> volume #185 level 0.2279
> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 5e-05, step 4, values float32
> volume #188 step 1
> volume #188 level 0.9982
> volume #188 color #ffffb280
> volume #188 color #ffffb266
> volume #185 level 0.2607
> show #!183 models
> hide #!183 models
> show #!183 models
> show #!182 models
> hide #!182 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!183 models
> volume #185 level 0.256
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!180 models
> hide #!180 models
> show #!177 models
> hide #!177 models
> show #!178 models
> hide #!178 models
> show #!179 models
> hide #!179 models
> show #!180 models
> show #!182 models
> hide #!182 models
> close #180
> show #!181 models
> hide #!181 models
> show #!179 models
> hide #!179 models
> show #!181 models
> hide #!181 models
> show #!182 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!179 models
> hide #!179 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> show #!183 models
> hide #!183 models
> show #!184 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!184 models
> volume #185 level 0.2841
> show #!184 models
> volume #184 level 0.7159
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!185 models
> show #!185 models
> hide #!182 models
> volume #185 level 0.3076
> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map.mrc
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.0442, step 4, values float32
> hide #!185 models
> volume #180 level 0.09552
> volume #180 step 1
> volume #180 level 0.2625
> show #!182 models
> hide #!182 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!180 models
> show #!180 models
> hide #!185 models
> volume #180 level 0.2996
> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map_sharp.mrc
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.217, step 4, values float32
> volume #189 step 1
> volume #189 level 0.3
> volume #189 level 0.7605
> hide #!189 models
> show #!185 models
> volume #185 level 0.31
> volume #180 level 0.31
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> select add #180
2 models selected
> color #180.1 cornflower blue
> select subtract #180
Nothing selected
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> hide #!180 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map.mrc
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.109, step 4, values float32
> volume #190 level 0.1683
> volume #190 step 1
> volume #190 level 0.1911
> volume #190 level 0.3013
> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map_sharp.mrc
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.211, step 4, values float32
> volume #191 level 0.2508
> volume #191 step 1
> volume #191 level 0.4399
> volume #191 color #005493
> volume #191 color #009193
> select add #191
2 models selected
> ui tool show "Color Actions"
> color sel medium blue
> color sel light sea green
> select subtract #191
Nothing selected
> volume #191 level 0.3926
> show #!182 models
> hide #!182 models
> show #!182 models
> show #!181 models
> hide #!181 models
> hide #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> volume #191 level 0.39
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> volume #182 level 0.39
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J811_volume_map.mrc
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.00828, step 4, values float32
> hide #!191 models
> volume #192 level 0.03286
> volume #192 step 1
> volume #192 color #4f8f00
> volume #192 color #009051
> volume #192 level 0.07832
> volume #192 level 0.1052
> volume #192 level 0.1
> volume #192 level 0.3
> volume #192 level 0.15
> volume #192 level 0.12
> volume #192 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 5e-05, step 4, values float32
> volume #193 step 1
> volume #193 color #e5bf9980
> volume #193 color #e5bf9967
> volume #193 color #e5bf9966
> volume #193 level 1
> volume #192 level 0.1186
> volume #193 level 0.5009
> volume #193 level 1
> volume #192 level 0.1434
> volume #192 level 0.1217
> close #193
> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 5e-05, step 4, values float32
> volume #193 level 1
> volume #193 step 1
> volume #193 color #99bfe574
> volume #193 color #99bfe567
> volume #193 color #99bfe566
> volume #192 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J812_volume_map.mrc
Opened cryosparc_P17_J812_volume_map.mrc as #194, grid size 520,520,520, pixel
0.95, shown at level 0.0198, step 4, values float32
> volume #194 level 0.05264
> volume #194 step 1
> volume #194 level 0.09845
> volume #194 level 0.1
> volume #194 level 0.12
> close #194
> show #!189 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J805_008_volume_map.mrc
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.0442, step 4, values float32
> hide #!189 models
> volume #194 level 0.2318
> volume #194 step 1
> volume #194 level 0.1158
> volume #194 level 0.3478
> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_00_00116_volume.mrc
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.0447, step 2, values float32
> hide #!194 models
> volume #195 level 0.2559
> volume #195 step 1
> volume #195 level 0.2828
> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_04_00116_volume.mrc
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.0135, step 2, values float32
> volume #196 step 1
> volume #196 level 0.1881
> volume #196 level 0.2658
> volume #196 level 0.2887
> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map.mrc
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.108, step 4, values float32
> hide #!195 models
> hide #!196 models
> volume #197 level 0.1961
> volume #197 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map_sharp.mrc
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
> volume #198 level 0.3147
> volume #198 step 1
> volume #198 level 0.4907
> volume #198 level 0.46
> volume #198 level 0.4
> volume #198 level 0.36
> volume #198 level 0.46
> open /Users/cvetkom/Downloads/cryosparc_P17_J822_volume_map.mrc
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.121, step 4, values float32
> hide #!199 models
> show #!199 models
> hide #!198 models
> volume #199 step 1
> volume #199 level 0.12
> volume #199 level 0.15
> volume #199 level 0.16
> volume #199 level 0.15
> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> volume #200 step 1
> volume #200 color #b2ffb283
> volume #200 color #b2ffb26c
> volume #200 color #b2ffb26b
> volume #200 level 1
> close #200
> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> color #200 #e5bf996b models
> color #200 #e5bf9968 models
> color #200 #e5bf9967 models
> color #200 #e5bf9966 models
> volume #200 step 1
> volume #200 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J824_005_volume_map_sharp.mrc
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.191, step 4, values float32
> hide #!200 models
> hide #!199 models
> volume #201 level 0.4868
> volume #201 step 1
> volume #201 level 0.46
> volume #201 level 0.4
> volume #201 level 0.38
> volume #201 level 0.3
> volume #201 level 0.32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class001.mrc
Opened Cl3D_j718_run_it025_class001.mrc as #202, grid size 520,520,520, pixel
0.95, shown at level 7.31e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class002.mrc
Opened Cl3D_j718_run_it025_class002.mrc as #203, grid size 520,520,520, pixel
0.95, shown at level 6.19e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class003.mrc
Opened Cl3D_j718_run_it025_class003.mrc as #204, grid size 520,520,520, pixel
0.95, shown at level 5.74e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class004.mrc
Opened Cl3D_j718_run_it025_class004.mrc as #205, grid size 520,520,520, pixel
0.95, shown at level 1.81e-06, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class005.mrc
Opened Cl3D_j718_run_it025_class005.mrc as #206, grid size 520,520,520, pixel
0.95, shown at level 5.25e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class006.mrc
Opened Cl3D_j718_run_it025_class006.mrc as #207, grid size 520,520,520, pixel
0.95, shown at level 2.64e-07, step 4, values float32
> hide #!201 models
> hide #!203 models
> hide #!204 models
> hide #!205 models
> hide #!206 models
> hide #!207 models
> volume #202 step 1
> volume #202 level 0.001537
> volume #203 step 1
> volume #203 level 0.00429
> hide #!203 models
> show #!205 models
> volume #205 step 1
> volume #205 level 0.006238
> volume #205 level 0.007973
> hide #!205 models
> show #!205 models
> hide #!205 models
> volume #206 step 1
> volume #206 level 0.003432
> volume #206 level 0.004328
> volume #202 level 0.001682
> show #!205 models
> hide #!205 models
> show #!205 models
> hide #!205 models
> volume #202 level 0.001267
> volume #203 level 0.004002
> volume #204 step 1
> volume #204 level 0.004153
> volume #204 level 0.003947
> volume #206 level 0.004481
> volume #207 step 1
> volume #207 level 0.00211
> hide #!207 models
> show #!205 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J828_volume_map.mrc
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.14, step 4, values float32
> hide #!205 models
> volume #208 step 1
> volume #208 level 0.1685
> volume #208 level 0.1611
> volume #208 level 0.08448
> open /Users/cvetkom/Downloads/cryosparc_P17_J829_class_00_final_volume.mrc
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.585, step 1, values float32
> hide #!208 models
> volume #209 level 0.5
> volume #209 level 0.4
> volume #209 level 0.45
> volume #209 level 0.5
> open /Users/cvetkom/Downloads/cryosparc_P17_J830_mask.mrc
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #210 color #e5bf9975
> volume #210 color #e5bf9967
> volume #210 color #e5bf9966
> volume #210 level 1
[Repeated 1 time(s)]
> hide #!210 models
> hide #!209 models
> show #!201 models
> hide #!201 models
> show #!201 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J825_006_volume_map_sharp.mrc
Opened cryosparc_P17_J825_006_volume_map_sharp.mrc as #211, grid size
588,588,588, pixel 0.95, shown at level 0.189, step 4, values float32
> volume #211 step 1
> volume #211 level 0.3194
> volume #211 level 0.32
> hide #!201 models
> show #!201 models
> hide #!201 models
> show #!201 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> color #211 #ff40ffff models
> color #211 #7a81ffff models
> hide #!201 models
> show #!201 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> show #!202 models
> hide #!201 models
> hide #!202 models
> volume #211 level 0.35
> show #!201 models
> hide #!211 models
> volume #201 level 0.35
> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_map_sharp.mrc
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
> hide #!201 models
> volume #212 level 0.4011
> volume #212 step 1
> show #!201 models
> hide #!201 models
> show #!211 models
> hide #!211 models
> show #!211 models
> select add #211
2 models selected
> ui mousemode right "rotate selected models"
Drag select of 211 cryosparc_P17_J825_006_volume_map_sharp.mrc , 212
cryosparc_P17_J831_007_volume_map_sharp.mrc
> select subtract #212
2 models selected
> view matrix models
> #211,0.99974,0.0073342,0.021665,-7.9265,-0.0059368,0.99794,-0.063871,19.839,-0.022089,0.063726,0.99772,-10.804
> view matrix models
> #211,-0.83053,-0.50843,-0.22743,701.17,-0.55206,0.80558,0.21509,144.3,0.073856,0.30419,-0.94974,435.51
> select subtract #211
Nothing selected
> ui tool show "Fit in Map"
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
correlation = 0.5456, correlation about mean = 0.05943, overlap = 5.974e+04
steps = 436, shift = 6.8, angle = 10.9 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.89957058 -0.40667531 -0.15933603 680.38831906
-0.42615436 0.89716922 0.11610278 108.46539449
0.09573525 0.17234438 -0.98037349 475.76940193
Axis 0.21472534 -0.97383892 -0.07436926
Axis point 336.07482386 0.00000000 256.67979639
Rotation angle (degrees) 172.47482888
Shift along axis 5.08617368
Correlation = 0.5456, Correlation about mean = 0.05943, Overlap = 5.974e+04
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
correlation = 0.5457, correlation about mean = 0.0594, overlap = 5.974e+04
steps = 44, shift = 0.0378, angle = 0.0389 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.89980651 -0.40634880 -0.15883608 680.25943553
-0.42572683 0.89739120 0.11595559 108.32590029
0.09541969 0.17195838 -0.98047203 475.96728322
Axis 0.21451210 -0.97389690 -0.07422527
Axis point 336.02953423 0.00000000 256.71123961
Rotation angle (degrees) 172.49947586
Shift along axis 5.09681985
> select add #211
2 models selected
> view matrix models
> #211,-0.90089,-0.40799,-0.14811,678.04,-0.41938,0.90616,0.054752,121.11,0.11187,0.11144,-0.98745,489.99
> volume #211 level 0.4
> select subtract #211
Nothing selected
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 381853 points
correlation = 0.9767, correlation about mean = 0.8803, overlap = 1.862e+05
steps = 388, shift = 8.54, angle = 19 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.97678811 -0.20990860 -0.04270100 623.15903654
-0.20103231 0.96714269 -0.15563105 99.70859450
0.07396625 -0.14343428 -0.98689189 576.21341964
Axis 0.10368016 -0.99174448 0.07545400
Axis point 308.25071118 0.00000000 301.13328663
Rotation angle (degrees) 176.62796126
Shift along axis 9.20139044
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!211 models
> volume #212 level 0.4
> volume #212 level 0.38
> volume #212 level 0.35
> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_mask_refine.mrc
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 4, values float32
> volume #213 color #b2b2b259
> volume #213 step 1
> volume #213 level 1
> volume #212 level 0.2391
> close #211
> open /Users/cvetkom/Downloads/cryosparc_P17_J843_008_volume_map_sharp.mrc
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.249, step 4, values float32
> hide #!211 models
> hide #!212 models
> hide #!213 models
> show #!211 models
> volume #211 level 0.7129
> volume #211 step 1
> volume #211 level 0.5829
> volume #211 level 0.56
> volume #211 level 0.55
> volume #211 level 0.5
> show #!194 models
> hide #!194 models
> show #!189 models
> hide #!189 models
> show #!189 models
> hide #!189 models
> show #!189 models
> hide #!189 models
> volume #211 level 0.55
> show #!189 models
> hide #!189 models
> show #!189 models
> volume #189 level 0.6
> hide #!189 models
> show #!189 models
> hide #!189 models
> ui mousemode right zoom
> hide #!211 models
> show #!210 models
> hide #!210 models
> show #!202 models
> hide #!202 models
> show #!203 models
> hide #!203 models
> show #!204 models
> hide #!204 models
> show #!205 models
> hide #!205 models
> show #!206 models
> hide #!206 models
> show #!207 models
> close #202-207
> show #!176 models
> hide #!176 models
> show #!129 models
> hide #!129 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> show #!135 models
> hide #!134 models
> hide #!133 models
> show #!133 models
> hide #!135 models
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> hide #!133 models
> show #!133 models
> show #!134 models
> hide #!134 models
> hide #!133 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!131 models
> hide #!131 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!110 models
> show #!111 models
> hide #!110 models
> hide #!111 models
> show #!112 models
> show #!120 models
> hide #!120 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!112 models
> show #!112 models
> hide #!133 models
> show #!134 models
> hide #!112 models
> show #!113 models
> hide #!113 models
> show #!113 models
> hide #!113 models
> show #!110 models
> hide #!110 models
> show #!111 models
> hide #!111 models
> show #!112 models
> hide #!112 models
> show #!113 models
> hide #!113 models
> show #!114 models
> hide #!114 models
> show #!115 models
> hide #!115 models
> show #!115 models
> hide #!115 models
> show #!115 models
> hide #!115 models
> hide #!134 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!71 models
> hide #!71 models
> show #!130 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> hide #!130 models
> show #!110 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> hide #!98 models
> show #!105 models
> show #!106 models
> hide #!105 models
> hide #!106 models
> show #!117 models
> show #!118 models
> hide #!117 models
> hide #!118 models
> show #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!70 models
> show #!71 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!70 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!130 models
> hide #!130 models
> show #!130 models
> show #!98 models
> hide #!98 models
> hide #!130 models
> show #!130 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!130 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> show #!129 models
> show #!130 models
> hide #!98 models
> hide #!99 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!139 models
> hide #!139 models
> show #!139 models
> hide #!139 models
> show #!139 models
> hide #!130 models
> show #!138 models
> hide #!139 models
> show #!143 models
> hide #!143 models
> show #!143 models
> hide #!138 models
> hide #!143 models
> show #!141 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> hide #!147 models
> show #!140 models
> hide #!140 models
> show #!145 models
> show #!146 models
> hide #!146 models
> show #!146 models
> hide #!145 models
> hide #!146 models
> show #!148 models
> hide #!148 models
> show #!157 models
> hide #!157 models
> show #!161 models
> hide #!161 models
> show #!174 models
> hide #!174 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.346, step 2, values float32
> volume #202 step 1
> volume #202 level 0.3331
> show #!157 models
> hide #!157 models
> show #!157 models
> hide #!157 models
> show #!161 models
> volume #161 level 0.32
> volume #161 level 0.34
> hide #!161 models
> show #!160 models
> hide #!160 models
> show #!159 models
> show #!161 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!160 models
> show #!173 models
> show #!175 models
> show #!157 models
> hide #!157 models
> hide #!160 models
> volume #173 level 0.3031
> volume #173 level 0.3465
> show #!175 models
> hide #!173 models
> volume #175 level 0.3281
> hide #!175 models
> show #!172 models
> hide #!172 models
> close #155-156,159-160,173,175-176
> show #!157 models
> show #!174 models
> hide #!174 models
> show #!174 models
> volume #174 level 0.3294
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> hide #!157 models
> show #!161 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> show #!161 models
> select add #161
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #161,-0.80087,-0.4765,-0.3627,729.62,0.10949,-0.71198,0.69361,276.28,-0.58874,0.51578,0.62238,115.15
> view matrix models
> #161,-0.84255,0.43705,-0.31481,469.51,-0.49419,-0.85972,0.12908,627.85,-0.21423,0.26433,0.94034,2.6659
> view matrix models
> #161,-0.91542,-0.17496,-0.36248,675.94,0.17298,-0.98418,0.038186,498.42,-0.36343,-0.027746,0.93121,129.94
> view matrix models
> #161,-0.95897,-0.26467,-0.1016,649.01,0.27072,-0.9613,-0.051053,486.58,-0.084153,-0.076463,0.99351,49.911
> view matrix models
> #161,-0.99187,0.12321,0.03177,514.81,-0.12543,-0.98874,-0.081553,613.22,0.021365,-0.084875,0.99616,22.011
> ui mousemode right zoom
> select clear
> hide #!161 models
> show #!161 models
> fitmap #161 inMap #141
Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
cryosparc_P17_J685_007_volume_map.mrc using 269413 points
correlation = 0.9961, correlation about mean = 0.9593, overlap = 9.415e+04
steps = 112, shift = 3.83, angle = 9.13 degrees
Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
Matrix rotation and translation
-0.99974072 -0.02276472 -0.00050563 565.44941758
0.02276965 -0.99929232 -0.02994005 559.04447071
0.00017631 -0.02994380 0.99955157 8.32772983
Axis -0.00008235 -0.01497460 0.99988787
Axis point 279.54196619 282.80415641 0.00000000
Rotation angle (degrees) 178.69527744
Shift along axis -0.09123841
> hide #!141 models
> show #!141 models
> volume #161 level 0.36
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> show #!147 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> show #!141 models
> select add #147
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #147,0.75391,-0.62474,-0.20327,302.4,-0.65039,-0.66601,-0.36528,749.91,0.092824,0.40759,-0.90843,455.15
> view matrix models
> #147,-0.31245,-0.67282,-0.67059,759.97,-0.54055,0.70643,-0.45691,373.58,0.78114,0.21972,-0.58441,212.49
> view matrix models
> #147,-0.90083,-0.32948,-0.28274,711.29,-0.41209,0.85388,0.3179,56.872,0.13669,0.40289,-0.90498,443.04
> view matrix models
> #147,-0.99864,0.030742,-0.042093,565.93,0.029267,0.99895,0.035202,-18.858,0.043131,0.033922,-0.99849,598.86
> ui mousemode right "translate selected models"
> view matrix models
> #147,-0.99864,0.030742,-0.042093,560.75,0.029267,0.99895,0.035202,-44.757,0.043131,0.033922,-0.99849,550.76
> view matrix models
> #147,-0.99864,0.030742,-0.042093,571.25,0.029267,0.99895,0.035202,-21.366,0.043131,0.033922,-0.99849,539.43
> select subtract #147
Nothing selected
> fitmap #147 inMap #141
Fit map cryosparc_P17_J690_006_volume_map.mrc in map
cryosparc_P17_J685_007_volume_map.mrc using 254434 points
correlation = 0.9983, correlation about mean = 0.9814, overlap = 9.297e+04
steps = 84, shift = 10.7, angle = 2.98 degrees
Position of cryosparc_P17_J690_006_volume_map.mrc (#147) relative to
cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
Matrix rotation and translation
-0.99966375 0.02590789 -0.00108426 552.09827323
0.02590403 0.99965851 0.00344015 -9.28972053
0.00117301 0.00341091 -0.99999349 555.06217083
Axis -0.01295398 -0.99991463 -0.00171281
Axis point 275.95266832 0.00000000 277.69485205
Rotation angle (degrees) 179.93532851
Shift along axis 1.18634199
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!141 models
> show #!157 models
> hide #!157 models
> show #!161 models
> hide #!161 models
> show #!161 models
> color #161 #00fa92ff models
> hide #!161 models
> show #!161 models
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!161 models
> hide #!147 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> ui mousemode right zoom
> lighting full
> lighting soft
> lighting simple
> lighting full
> hide #!32 models
> show #!32 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!95 models
> hide #!95 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J517_006_volume_map_zflip.mrc
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #155 step 1
> lighting soft
> show #!179 models
> hide #!179 models
> show #!179 models
> hide #!179 models
> show #!179 models
> select add #155
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #155,-0.98089,0.19377,-0.017464,502.92,0.10481,0.60192,0.79165,-107.18,0.16391,0.77469,-0.61072,122.66
> view matrix models
> #155,-0.25052,0.96798,-0.015979,76.052,0.96671,0.24923,-0.057953,-41.024,-0.052115,-0.029966,-0.99819,507.99
> view matrix models
> #155,0.96775,0.17696,-0.17931,1.7558,0.20922,-0.96102,0.18073,460.27,-0.14034,-0.21242,-0.96705,577.47
> view matrix models
> #155,0.96767,0.091902,-0.2349,39.67,0.12427,-0.9841,0.12691,503.72,-0.2195,-0.152,-0.9637,581.47
> view matrix models
> #155,0.91176,0.40771,0.049574,-104.32,0.37999,-0.79159,-0.47852,523.82,-0.15586,0.45514,-0.87667,368.35
> lighting simple
> view matrix models
> #155,0.92481,0.37946,0.027133,-94.419,0.34082,-0.79474,-0.50223,541.44,-0.16901,0.47372,-0.86431,363.7
> view matrix models
> #155,0.94675,0.28168,0.15598,-103.76,0.32196,-0.82268,-0.46855,546.56,-0.0036582,0.49382,-0.86956,312.94
> view matrix models
> #155,0.9947,0.045724,-0.092058,10.698,0.043566,-0.99873,-0.02532,567.43,-0.093098,0.021175,-0.99543,504.12
> ui mousemode right "translate selected models"
> view matrix models
> #155,0.9947,0.045724,-0.092058,46.226,0.043566,-0.99873,-0.02532,564.24,-0.093098,0.021175,-0.99543,557.75
> view matrix models
> #155,0.9947,0.045724,-0.092058,13.547,0.043566,-0.99873,-0.02532,566.45,-0.093098,0.021175,-0.99543,563.81
> select subtract #155
Nothing selected
> fitmap #155 inMap #179
Fit map cryosparc_P17_J517_006_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2026669 points
correlation = 0.9972, correlation about mean = 0.9729, overlap = 1.474e+05
steps = 220, shift = 19.3, angle = 6.44 degrees
Position of cryosparc_P17_J517_006_volume_map_zflip.mrc (#155) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#179) coordinates:
Matrix rotation and translation
0.99982429 0.01272017 0.01376969 -7.71473943
0.01281628 -0.99989397 -0.00691402 556.62008375
0.01368028 0.00708928 -0.99988130 552.40010778
Axis 0.99995607 0.00638455 0.00686279
Axis point 0.00000000 277.36764127 277.20094376
Rotation angle (degrees) 179.59881412
Shift along axis -0.36962502
> ui mousemode right zoom
> lighting soft
> hide #!179 models
> show #!179 models
> hide #!179 models
> show #!179 models
> show #!178 models
> hide #!179 models
> show #!179 models
> hide #!178 models
> volume #179 level 0.16
> hide #!179 models
> show #!179 models
> hide #!179 models
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J851_volume_map.mrc
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.179, step 4, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J854_volume_map.mrc
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.178, step 4, values float32
> hide #!156 models
> show #!156 models
> hide #!156 models
> hide #!159 models
> show #!159 models
> show #!156 models
> volume #156 step 1
> volume #159 step 1
> volume #156 level 0.15
> volume #159 level 0.15
> volume #156 level 0.12
> volume #156 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J857_mask.mrc
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> volume #160 step 1
> volume #160 color #b2ffb260
> volume #160 color #b2ffb261
> volume #160 level 1
> volume #160 color #b2ffb270
> volume #160 level 1
> volume #156 level 0.08
> volume #156 level 0.1
> volume #156 level 0.9
> volume #156 level 0.09
> volume #156 level 0.08
> open /Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 4, values float32
> volume #173 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J866_class_00_00042_volume.mrc
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 1.71, step 1, values float32
> volume #175 level 1.364
> volume #175 level 1
> volume #175 level 0.9
> volume #175 level 0.8
> volume #175 level 0.9
> open /Users/cvetkom/Downloads/cryosparc_P17_J869_mask.mrc
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #176 color #cccc9964
> volume #176 color #cccc9963
> volume #176 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J870_mask.mrc
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #203 color #b2b2b267
> volume #203 color #b2b2b266
> volume #203 level 1
[Repeated 1 time(s)]
> show #!213 models
> hide #!213 models
> show #!213 models
> hide #!213 models
> hide #!203 models
> show #!203 models
> hide #!203 models
> show #!211 models
> hide #!211 models
> show #!212 models
> hide #!212 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J867_007_volume_map.mrc
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J871_007_volume_map.mrc
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> volume #204 step 1
> volume #205 step 1
> volume #205 level 0.2369
> volume #205 level 0.1513
> show #!130 models
> hide #!130 models
> show #!130 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> volume #129 level 0.01525
> volume #129 level 0.02295
> volume #129 level 0.02195
> volume #129 level 0.02859
> volume #129 level 0.01548
> volume #129 level 0.01394
> volume #129 level 0.02201
> volume #129 level 0.02491
> volume #129 level 0.02207
> volume #129 level 0.01258
> volume #129 level 0.01323
> show #!74 models
> volume #129 level 0.014
> hide #!74 models
> show #!74 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!122 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!122 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> hide #!123 models
> show #!122 models
> show #!123 models
> hide #!122 models
> show #!122 models
> show #!124 models
> hide #!123 models
> hide #!122 models
> hide #!124 models
> show #!124 models
> show #!123 models
> hide #!123 models
> show #!122 models
> hide #!122 models
> hide #!124 models
> show #!124 models
> hide #!124 models
> show #!125 models
> hide #!125 models
> show #!125 models
> hide #!125 models
> show #!126 models
> show #!127 models
> show #!134 models
> show #!135 models
> hide #!135 models
> show #!128 models
> hide #!128 models
> show #!135 models
> hide #!135 models
> show #!133 models
> hide #!127 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!129 models
> show #!130 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> hide #!133 models
> hide #!134 models
> show #!122 models
> show #!123 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!130 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> hide #!130 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!133 models
> show #!134 models
> show #!104 models
> hide #!104 models
> show #!103 models
> hide #!103 models
> show #!103 models
> show #!102 models
> hide #!102 models
> show #!104 models
> hide #!104 models
> show #!102 models
> hide #!103 models
> show #!103 models
> hide #!102 models
> show #!101 models
> hide #!101 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!103 models
> show #!103 models
> hide #!100 models
> show #!100 models
> hide #!133 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!103 models
> show #!103 models
> hide #!103 models
> show #!103 models
> hide #!103 models
> show #!103 models
> hide #!100 models
> hide #!103 models
> show #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> show #!100 models
> hide #!100 models
> show #!101 models
> hide #!101 models
> show #!102 models
> hide #!102 models
> show #!103 models
> hide #!103 models
> show #!104 models
> hide #!104 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J876_class_00_final_volume.mrc
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.504, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J880_class_00_final_volume.mrc
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
> hide #!98 models
> hide #!99 models
> hide #!129 models
> hide #!130 models
> volume #206 level 0.3476
> open /Users/cvetkom/Downloads/cryosparc_P17_J874_volume_map.mrc
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.404, step 2, values float32
> volume #214 step 1
> volume #214 level 0.3304
> open /Users/cvetkom/Downloads/cryosparc_P17_J882_volume_map.mrc
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.4, step 2, values float32
> volume #215 step 1
> volume #215 level 0.347
> volume #215 level 0.3003
> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_00_00042_volume.mrc
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 0.839, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_01_00042_volume.mrc
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
> volume #216 level 1.25
> volume #217 level 1.171
> volume #217 level 1
> volume #217 level 0.9
> volume #217 level 0.8
> volume #217 level 0.85
> volume #217 level 0.8
> open /Users/cvetkom/Downloads/cryosparc_P17_J883_mask.mrc
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #218 color #cccc9967
> volume #218 color #cccc9969
> volume #218 level 1
> volume #218 level 0.5107
> volume #218 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J885_008_volume_map.mrc
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> hide #!217 models
> hide #!218 models
> volume #219 step 1
> volume #220 step 1
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.00502, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.00208, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job519.mrc
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 5e-05, step 4, values float32
> hide #!218 models
> hide #!220 models
> volume #223 step 1
> volume #223 level 0.9925
> volume #223 color #ffb2ff80
> volume #223 color #ffb2ff66
> volume #222 step 1
> volume #221 step 1
> volume #222 level 0.002458
> volume #222 level 0.003951
> volume #222 level 0.004587
> volume #222 level 0.005
> volume #222 level 0.004508
> volume #222 level 0.0045
> volume #221 level 0.0045
> hide #!223 models
> hide #!221 models
> show #!221 models
> hide #!222 models
> hide #!221 models
> show #!222 models
> ui tool show "Map Eraser"
> hide #224 models
> show #224 models
> hide #!222 models
Drag select of eraser sphere, 87 of 1000 triangles
> select clear
> show #!222 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> ui mousemode right zoom
> select add #224
1 model selected
> ui mousemode right "translate selected models"
> hide #224 models
> show #224 models
> hide #!222 models
> show #!222 models
> select subtract #224
Nothing selected
> select add #224
1 model selected
> select subtract #224
Nothing selected
> ui mousemode right zoom
Drag select of eraser sphere, 27 of 1000 triangles
> select #224
1 model selected
> select #224
1 model selected
> select clear
> ui mousemode right "map eraser"
> volume erase #222 center 235.13,229.91,259.65 radius 50.358
Opened Ref3D_job506_run_class001_NCP.mrc copy as #225, grid size 588,588,588,
pixel 0.95, shown at step 1, values float32
> volume erase #225 center 240.34,217.6,249.39 radius 50.274
> volume erase #225 center 249.31,217.92,185.58 radius 50.274
> volume erase #225 center 254.34,196.31,201.83 radius 50.274
> volume erase #225 center 244.51,226.1,178.85 radius 50.274
> volume erase #225 center 266.29,219.21,231.39 radius 71.221
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> ui mousemode right zoom
> vop gaussian #225 sdev 2.85
Opened Ref3D_job506_run_class001_NCP.mrc copy gaussian as #224, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> volume #224 level 0.004498
> volume #224 level 0.004
> volume #224 level 0.0045
> save
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_bareNCP.mrc
> models #224
> hide #!224 models
> show #!224 models
> show #!222 models
> hide #!222 models
> hide #!225 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!224 models
> show #!224 models
> hide #!224 models
> show #!224 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> lighting full
> hide #!222 models
> show #!222 models
> color #224 #d6d6d6ff models
> color #224 darkgrey models
> hide #!224 models
> show #!224 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> hide #!224 models
> show #!222 models
> show #!223 models
> show #!221 models
> volume #223 level 0.5133
> volume #223 level 1
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!224 models
> hide #!222 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job744/mask.mrc
Opened mask.mrc as #226, grid size 588,588,588, pixel 0.95, shown at level
5e-05, step 4, values float32
> hide #!224 models
> show #!224 models
> hide #!221 models
> volume #226 step 1
> volume #226 color #e5bf9966
> volume #226 level 1
> volume #226 level 0.3859
> volume #226 level 0.5044
> hide #!224 models
> show #!221 models
> volume #226 level 1
> hide #!226 models
> show #!226 models
> volume #226 level 1
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> volume #226 level 1
> hide #!221 models
> hide #!226 models
> show #!219 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> close #219-220
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J884_009_volume_map.mrc
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J885_008_volume_map.mrc
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> volume #219 step 1
> volume #220 step 1
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J888_009_volume_map.mrc
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 2, values float32
> volume #227 step 1
> volume #219 level 0.4485
> volume #219 level 0.4625
> volume #219 step 2
> volume #219 step 1
> show #!213 models
> hide #!213 models
> volume #227 step 2
> volume #227 step 1
> close #225
> close #226
> hide #!219 models
> show #!219 models
> volume #219 step 2
> volume #219 step 4
> volume #219 step 1
> volume #219 step 2
> volume #219 level 0.4261
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
\u2014\u2014\u2014 End of log from Thu Jul 11 13:31:37 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!219 models
> show #!227 models
> hide #!227 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J984_class_00_00062_volume_sharp.mrc
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 0.37, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_00400_volume.mrc
Opened cryosparc_P17_J967_class_00_00400_volume.mrc as #226, grid size
128,128,128, pixel 3.27, shown at level 0.384, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J981_class_00_00062_volume_sharp.mrc
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 0.327, step 1, values float32
> show #!227 models
> hide #!227 models
> hide #!225 models
> hide #!228 models
> volume #226 level 1.133
> volume #226 level 1.3
> volume #226 level 1.35
> lighting soft
> volume #226 color darkgrey
> volume #226 level 1.4
> volume #226 level 1.45
> volume #225 level 2.008
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!228 models
> volume #228 level 1.823
> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_final_volume.mrc
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.197, step 1, values float32
> close #226
> volume #229 level 1.053
> volume #229 level 1
> volume #229 level 0.9
> volume #229 level 0.8
> show #!228 models
> show #!227 models
> hide #!227 models
> show #!225 models
> hide #!229 models
> show #!229 models
> hide #!228 models
> hide #!229 models
> show #!229 models
> volume #225 level 1.9
> volume #225 level 1.8
> hide #!229 models
> show #!229 models
> volume #225 level 1.6
> show #!211 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!198 models
> hide #!198 models
> show #!197 models
> hide #!197 models
> show #!191 models
> hide #!191 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
> hide #!225 models
> volume #226 level 0.2956
> volume #226 step 1
> volume #226 level 0.334
> show #!230 models
> hide #!226 models
> volume #226 level 0.33
> show #!226 models
> hide #!230 models
> hide #!226 models
> show #!230 models
> volume #230 step 1
> volume #230 level 0.33
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> volume #230 level 0.32
> volume #230 level 0.3
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!231 models
> hide #!230 models
> volume #231 step 2
> volume #231 step 1
> volume #231 level 0.3
> show #!191 models
> hide #!191 models
> show #!190 models
> show #!191 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!198 models
> hide #!191 models
> open 1ID3 fromDatabase pdb format mmcif
1id3 title:
Crystal structure of the yeast nucleosome core particle reveals fundamental
differences In inter-nucleosome interactions [more info...]
Chain information for 1id3 #232
---
Chain | Description | UniProt
A E | HISTONE H3 | H3_YEAST 1-135
B F | HISTONE H4 | H4_YEAST 1-102
C G | HISTONE H2A.1 | H2A1_YEAST 1-131
D H | HISTONE H2B.2 | H2B2_YEAST 1-130
I J | PALINDROMIC 146BP DNA FRAGMENT |
Non-standard residues in 1id3 #232
---
MN \u2014 manganese (II) ion
> hide #!232 models
> show #!232 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view sel
> select subtract #232
Nothing selected
> show #!228 models
> hide #!228 models
> show #!225 models
> hide #!225 models
> lighting simple
> show #!229 models
> hide #!229 models
> show #!225 models
> show #!228 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!228 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #232,1,0,0,194.77,0,1,0,198.7,0,0,1,241.66
> select add #225
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 7 models selected
> view sel
> select subtract #225
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #232,0.45362,0.62002,-0.64016,176.82,-0.86856,0.46844,-0.16176,188.02,0.19958,0.62939,0.75102,238.14
> view matrix models
> #232,0.73516,0.67582,-0.053002,205.68,-0.43197,0.40677,-0.80495,150.64,-0.52244,0.61466,0.59097,235.27
> view matrix models
> #232,0.74922,0.65491,0.098772,212.99,-0.3682,0.53581,-0.75982,154.67,-0.55054,0.53291,0.64258,236.74
> view matrix models
> #232,0.63725,0.62725,-0.44773,185.38,-0.56763,-0.01092,-0.82321,143.6,-0.52125,0.77874,0.34909,225.69
> ui mousemode right "translate selected models"
> view matrix models
> #232,0.63725,0.62725,-0.44773,108.34,-0.56763,-0.01092,-0.82321,126.58,-0.52125,0.77874,0.34909,223.48
> ui mousemode right "rotate selected models"
> view matrix models
> #232,0.69009,0.70479,0.16445,140.62,-0.26062,0.454,-0.85204,130.7,-0.67517,0.54512,0.49698,228.24
> view matrix models
> #232,0.021212,0.98524,0.16984,150.87,-0.50552,0.15714,-0.84839,127.69,-0.86256,-0.067863,0.50139,219.42
> view matrix models
> #232,0.026211,0.99233,-0.12082,136.06,-0.53573,-0.088094,-0.83978,124.17,-0.84398,0.086736,0.52931,223.35
> view matrix models
> #232,0.0051654,0.11484,-0.99337,76.495,-0.63253,-0.76903,-0.092196,151.55,-0.77452,0.62881,0.068669,208.5
> view matrix models
> #232,0.026817,-0.97752,0.20912,119.22,-0.36995,0.18463,0.91052,217.22,-0.92866,-0.10178,-0.35669,175.39
> view matrix models
> #232,-0.0985,-0.93943,0.32829,126.94,0.94539,0.014666,0.32562,174.18,-0.31071,0.34244,0.88668,241.92
> view matrix models
> #232,0.23695,-0.92136,0.30814,123.63,0.84083,0.035592,-0.54013,130.99,0.48669,0.38708,0.78314,231.21
> view matrix models
> #232,0.37181,-0.91507,0.15625,114.91,0.42362,0.017477,-0.90567,115.18,0.82602,0.40293,0.39414,208.93
> view matrix models
> #232,0.30529,-0.94633,-0.10613,101.45,0.56154,0.26891,-0.78253,124.73,0.76907,0.1793,0.6135,216.78
> view matrix models
> #232,0.059237,0.85249,0.51938,166.21,0.47573,-0.48152,0.73609,190.34,0.8776,0.20348,-0.43407,162.69
> view matrix models
> #232,0.24626,-0.51664,-0.82003,72.694,0.61898,0.73489,-0.27712,158.16,0.7458,-0.43934,0.50076,200.59
> view matrix models
> #232,-0.067706,-0.98402,0.16471,117.56,0.51804,-0.17576,-0.83711,114.66,0.85268,0.028649,0.52165,208.85
> volume flip #225
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip as #233, grid
size 128,128,128, pixel 3.27, shown at step 1, values float32
> view matrix models
> #232,-0.086674,-0.98325,0.16032,117.49,0.60367,-0.17985,-0.77669,117.02,0.79251,0.02946,0.60914,213.81
> view matrix models
> #232,-0.20892,-0.97186,0.10878,115.99,0.81932,-0.11321,0.56205,185.07,-0.53392,0.20655,0.81992,237.89
> view matrix models
> #232,-0.0034667,-0.99986,-0.016272,107.52,0.52919,-0.015641,0.84836,203.66,-0.8485,-0.0056699,0.52917,221.79
> view matrix models
> #232,0.10405,-0.99333,-0.049687,105.09,0.51074,0.010501,0.85967,204.82,-0.85341,-0.11483,0.50843,218.9
> view matrix models
> #232,0.155,-0.97565,0.1552,115.49,0.4679,0.21087,0.85826,208.52,-0.87008,-0.060414,0.48919,218.98
> view matrix models
> #232,0.045605,-0.97983,0.19456,118.28,0.53868,0.18814,0.82123,205.68,-0.84127,0.067353,0.5364,223.36
> ui mousemode right "translate selected models"
> view matrix models
> #232,0.045605,-0.97983,0.19456,194.24,0.53868,0.18814,0.82123,258.89,-0.84127,0.067353,0.5364,231.26
> view matrix models
> #232,0.045605,-0.97983,0.19456,195.08,0.53868,0.18814,0.82123,259.08,-0.84127,0.067353,0.5364,236.86
> ui mousemode right "rotate selected models"
> view matrix models
> #232,-0.039543,-0.99451,0.096893,190.48,-0.23842,0.10356,0.96562,271.04,-0.97036,0.015082,-0.24121,197.13
> view matrix models
> #232,-0.078672,-0.98952,0.12105,192.1,-0.5971,0.14401,0.78913,265.46,-0.7983,-0.010198,-0.60217,176.87
> view matrix models
> #232,-0.14713,-0.98779,0.051262,189.09,-0.8147,0.15042,0.56004,255.52,-0.56091,0.040637,-0.82688,164.4
> select subtract #232
Nothing selected
> ui tool show "Fit in Map"
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 72
shifted from previous position = 12.2
rotated from previous position = 11.2 degrees
atoms outside contour = 5403, contour level = 1.6
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03585182 -0.99591182 0.08291139 194.40297797
-0.72260858 0.08314376 0.68623899 250.19258695
-0.69032709 -0.03530956 -0.72263528 174.98991176
Axis -0.66054809 0.70786809 0.25019790
Axis point 245.81431621 -0.00000000 -10.35559013
Rotation angle (degrees) 146.89506394
Shift along axis 92.47294040
> volume #233 level 1.5
> volume #233 level 1.4
> ui mousemode right "translate selected models"
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view matrix models
> #232,-0.035852,-0.99591,0.082911,187.84,-0.72261,0.083144,0.68624,334.95,-0.69033,-0.03531,-0.72264,195.33
> lighting soft
> view matrix models
> #232,-0.035852,-0.99591,0.082911,189.25,-0.72261,0.083144,0.68624,329.81,-0.69033,-0.03531,-0.72264,193.67
> lighting simple
> view matrix models
> #232,-0.035852,-0.99591,0.082911,207.89,-0.72261,0.083144,0.68624,254.31,-0.69033,-0.03531,-0.72264,174.46
> view matrix models
> #232,-0.035852,-0.99591,0.082911,196.79,-0.72261,0.083144,0.68624,255.92,-0.69033,-0.03531,-0.72264,174.52
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 52
shifted from previous position = 6.21
rotated from previous position = 0.0558 degrees
atoms outside contour = 4425, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03529330 -0.99599473 0.08215154 194.42252609
-0.72248530 0.08222358 0.68647963 250.18011940
-0.69048489 -0.03512516 -0.72249349 174.98679362
Axis -0.66080361 0.70753542 0.25046400
Axis point 245.92146757 -0.00000000 -10.42218197
Rotation angle (degrees) 146.90659877
Shift along axis 92.36408147
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 48
shifted from previous position = 0.0262
rotated from previous position = 0.0179 degrees
atoms outside contour = 4427, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03522647 -0.99601286 0.08196018 194.43601851
-0.72265585 0.08203483 0.68632267 250.16027535
-0.69030980 -0.03505228 -0.72266432 174.97347823
Axis -0.66086507 0.70749095 0.25042747
Axis point 245.92434501 0.00000000 -10.39497167
Rotation angle (degrees) 146.92196206
Shift along axis 92.30832410
> select subtract #232
Nothing selected
> hide #!232 atoms
> show #!232 cartoons
> hide #!233 models
> show #!233 models
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 44
shifted from previous position = 0.00249
rotated from previous position = 0.0128 degrees
atoms outside contour = 4428, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03534401 -0.99599682 0.08210439 194.44302789
-0.72273427 0.08221501 0.68621853 250.15752046
-0.69022169 -0.03508594 -0.72274684 174.96686637
Axis -0.66081898 0.70756214 0.25034793
Axis point 245.90230259 0.00000000 -10.37331191
Rotation angle (degrees) 146.92300591
Shift along axis 92.31293996
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 48
shifted from previous position = 0.0672
rotated from previous position = 0.0319 degrees
atoms outside contour = 4424, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03562336 -0.99595084 0.08254033 194.40523233
-0.72285407 0.08271076 0.68603274 250.17963983
-0.69008186 -0.03522582 -0.72287355 174.97000524
Axis -0.66069357 0.70774412 0.25016449
Axis point 245.83818539 0.00000000 -10.32676146
Rotation angle (degrees) 146.91829753
Shift along axis 92.39216339
> volume #233 color #b2b2b2db
> volume #233 color #b2b2b2b0
> volume #233 color #b2b2b29a
> volume #233 color #b2b2b299
> volume #233 color #b2b2b2b2
> volume #233 color #b2b2b2cc
> combine #232
> hide #!232 models
> hide #!234 models
> show #!234 models
> select #234/I
3006 atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
> delete atoms (#!234 & sel)
> delete bonds (#!234 & sel)
> select #234/J
3004 atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
> delete atoms (#!234 & sel)
> delete bonds (#!234 & sel)
> hide #!233 models
> show #!233 models
> fitmap #234 inMap #233
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 6114
atoms
average map value = 1.618, steps = 48
shifted from previous position = 0.869
rotated from previous position = 6.47 degrees
atoms outside contour = 2277, contour level = 1.4
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.05927763 -0.99809265 0.01724050 190.79692871
-0.66015313 0.05215041 0.74931847 251.66034038
-0.74878836 0.03303645 -0.66198534 180.19394497
Axis -0.65007489 0.69522355 0.30670320
Axis point 244.94027053 -0.00000000 -21.53118005
Rotation angle (degrees) 146.56966321
Shift along axis 106.19396109
> volume #233 color #b2b2b280
> volume #233 color #b2b2b29a
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!234 models
> hide #!233 models
> show #!233 models
> hide #!232 models
> hide #!233 models
> show #!129 models
> select add #129
4 models selected
> view clip false
> select subtract #129
Nothing selected
> show #!130 models
> show #!227 models
> hide #!227 models
> show #!227 models
> hide #!227 models
> show #!227 models
> hide #!227 models
> volume flip #227
Opened cryosparc_P17_J888_009_volume_map.mrc z flip as #235, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> select add #235
2 models selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #235,0.84663,0.46913,0.25127,-169.59,0.42608,-0.88042,0.20812,364.8,0.31886,-0.069133,-0.94528,519.57
> view matrix models
> #235,-0.53578,-0.80769,-0.24613,731.78,-0.84162,0.48737,0.23271,310.31,-0.067998,0.33183,-0.94089,508.65
> view matrix models
> #235,-0.9965,-0.022294,-0.080596,581.12,-0.043426,0.96162,0.27092,-58.716,0.071463,0.27347,-0.95922,492.67
> ui mousemode right "translate selected models"
> view matrix models
> #235,-0.9965,-0.022294,-0.080596,577.57,-0.043426,0.96162,0.27092,-52.189,0.071463,0.27347,-0.95922,460.39
> volume #235 step 2
> select subtract #235
Nothing selected
> fitmap #235 inMap #130
Fit map cryosparc_P17_J888_009_volume_map.mrc z flip in map
Cl3D_j591_run_it025_class002.mrc using 31742 points
correlation = 0.9449, correlation about mean = 0.3834, overlap = 384.9
steps = 216, shift = 20, angle = 24.3 degrees
Position of cryosparc_P17_J888_009_volume_map.mrc z flip (#235) relative to
Cl3D_j591_run_it025_class002.mrc (#130) coordinates:
Matrix rotation and translation
-0.97670485 -0.09877980 -0.19049983 628.35061820
-0.19630370 0.76986862 0.60726203 -34.18266636
0.08667462 0.63051159 -0.77132526 290.90888037
Axis 0.07887912 -0.94037367 -0.33087073
Axis point 301.47094386 0.00000000 176.26702948
Rotation angle (degrees) 171.52518698
Shift along axis -14.54501139
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!98 models
> show #!99 models
> show #!219 models
> hide #!219 models
> volume flip #219
Opened cryosparc_P17_J884_009_volume_map.mrc z flip as #236, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> select add #236
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.14,0.86518,0.48153,-32.729,-0.98201,-0.059076,-0.17936,602.39,-0.12673,-0.49797,0.85788,204
> view matrix models
> #236,-0.95021,0.22201,0.21868,433.84,-0.29489,-0.86749,-0.40063,679.42,0.10076,-0.44517,0.88976,117.62
> ui mousemode right "translate selected models"
> view matrix models
> #236,-0.95021,0.22201,0.21868,442.55,-0.29489,-0.86749,-0.40063,714.68,0.10076,-0.44517,0.88976,125.94
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.96826,0.24636,0.042262,487.62,-0.23836,-0.85916,-0.4528,710.28,-0.07524,-0.4485,0.89061,176.2
> ui mousemode right "translate selected models"
> view matrix models
> #236,-0.96826,0.24636,0.042262,471.31,-0.23836,-0.85916,-0.4528,704.57,-0.07524,-0.4485,0.89061,178.79
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> select clear
> fitmap #236 inMap #98
Fit map cryosparc_P17_J884_009_volume_map.mrc z flip in map
Cl3D_j581_run_it025_class001.mrc using 185363 points
correlation = 0.8766, correlation about mean = 0.02403, overlap = 2112
steps = 192, shift = 22.6, angle = 21.2 degrees
Position of cryosparc_P17_J884_009_volume_map.mrc z flip (#236) relative to
Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
Matrix rotation and translation
-0.84354066 0.50422936 0.18491053 314.97189258
-0.50932699 -0.64184531 -0.57325441 772.53341394
-0.17036775 -0.57774333 0.79824024 267.14568387
Axis -0.00417951 0.33079007 -0.94369511
Axis point 276.01471701 384.47498501 0.00000000
Rotation angle (degrees) 147.51935105
Shift along axis 2.12587651
> hide #!98 models
> hide #!99 models
> volume flip #236
Opened cryosparc_P17_J884_009_volume_map.mrc z flip z flip as #237, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> close #236
> show #!98 models
> show #!99 models
> select add #237
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #237,0.96723,0.12731,-0.21969,22.54,0.15273,-0.9829,0.10285,476.95,-0.20284,-0.13303,-0.97013,678.92
> view matrix models
> #237,0.98911,0.12697,-0.074375,-26.233,0.1345,-0.98512,0.10698,481.46,-0.059685,-0.11582,-0.99148,640.32
> view matrix models
> #237,0.99344,0.076053,-0.08539,-10.83,0.10378,-0.91318,0.39411,386.84,-0.048004,-0.40039,-0.91509,689.4
> ui mousemode right "translate selected models"
> view matrix models
> #237,0.99344,0.076053,-0.08539,-17.742,0.10378,-0.91318,0.39411,419.91,-0.048004,-0.40039,-0.91509,662.61
> view matrix models
> #237,0.99344,0.076053,-0.08539,-17.954,0.10378,-0.91318,0.39411,412.57,-0.048004,-0.40039,-0.91509,657.54
> ui mousemode right "rotate selected models"
> view matrix models
> #237,0.99498,0.052431,-0.085289,-12.206,0.089013,-0.85322,0.5139,365.78,-0.045827,-0.51891,-0.8536,670.02
> ui mousemode right "translate selected models"
> view matrix models
> #237,0.99498,0.052431,-0.085289,4.4691,0.089013,-0.85322,0.5139,363.94,-0.045827,-0.51891,-0.8536,680.57
> select subtract #237
Nothing selected
> fitmap #237 inMap #98
Fit map cryosparc_P17_J884_009_volume_map.mrc z flip z flip in map
Cl3D_j581_run_it025_class001.mrc using 185363 points
correlation = 0.9464, correlation about mean = 0.3043, overlap = 2607
steps = 148, shift = 5.24, angle = 12.2 degrees
Position of cryosparc_P17_J884_009_volume_map.mrc z flip z flip (#237)
relative to Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
Matrix rotation and translation
0.95506772 0.17454310 -0.23954199 25.26355402
0.28049806 -0.79336127 0.54027653 283.68421592
-0.09574180 -0.58319174 -0.80667274 694.76834568
Axis -0.98759585 -0.12640897 0.09314076
Axis point 0.00000000 249.94675701 303.67322404
Rotation angle (degrees) 145.33414419
Shift along axis 3.90083895
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> volume #237 step 2
> volume #237 level 0.3935
> volume #237 level 0.3609
> volume #237 level 0.3342
> show #!98 models
> show #!97 models
> hide #!97 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!173 models
> show #!205 models
> hide #!173 models
> ui mousemode right zoom
> lighting soft
> show #!204 models
> hide #!205 models
> show #!205 models
> hide #!204 models
> show #!204 models
> show #!206 models
> hide #!205 models
> hide #!206 models
> hide #!204 models
> show #!204 models
> show #!205 models
> hide #!204 models
> hide #!205 models
> show #!234 models
> hide #!234 models
> show #!234 models
> show #!228 models
> hide #!228 models
> show #!225 models
> hide #!225 models
> show #!233 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!233 models
> hide #!232 models
> show #!225 models
> show #!233 models
> show #!234 models
> hide #!234 models
> show #!234 models
> color #233 #b2b2b2b7 models
> color #233 #b2b2b2c0 models
> color #233 #b2b2b2c6 models
> color #233 #b2b2b2ca models
> color #233 #b2b2b2cb models
> color #233 #b2b2b2cc models
> color #233 #b2b2b2ff models
> color #233 #b2b2b2f3 models
> color #233 #b2b2b2ff models
> color #233 #b2b2b2ee models
> color #233 #b2b2b2a5 models
> color #233 #b2b2b2ff models
> color #233 #b2b2b283 models
> color #233 #b2b2b298 models
> color #233 #b2b2b2ff models
[Repeated 2 time(s)]
> color #233 #b2b2b216 models
> color #233 #b2b2b22a models
> color #233 #b2b2b268 models
> color #233 #b2b2b24e models
> color #233 #b2b2b27c models
> color #233 #b2b2b236 models
> color #233 #b2b2b280 models
> color #233 #b2b2b2ff models
> hide #!233 models
> show #!233 models
> select #234/A
807 atoms, 813 bonds, 102 residues, 1 model selected
> volume flip #236sel #234/A,E
Missing or invalid "volumes" argument: only initial part "#236" of atom
specifier valid
> select #234/A,E
1615 atoms, 1626 bonds, 205 residues, 1 model selected
> color sel orange
> select #234/B,F
1320 atoms, 1326 bonds, 173 residues, 1 model selected
> color sel orange red
> select clear
> show #!233 models
> hide #!237 models
> color #233 #b2b2b272 models
> color #233 #b2b2b27c models
> show #!179 models
> hide #!179 models
> show #!178 models
> hide #!178 models
> show #!179 models
> hide #!179 models
> combine #179
No structures specified
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> select add #236
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.012453,0.9963,-0.085041,38.532,-0.99954,-0.014744,-0.026367,562,-0.027524,0.084674,0.99603,-14.052
> view matrix models
> #236,0.059878,0.99536,-0.075321,15.571,-0.99446,0.066013,0.081795,504.47,0.086388,0.070006,0.9938,-41.09
> view matrix models
> #236,0.76783,0.50486,-0.39441,52.38,-0.29922,0.82696,0.47602,-20.228,0.56648,-0.24749,0.78603,-22.96
> lighting simple
> view matrix models
> #236,-0.88103,0.27074,-0.38793,573.03,-0.025569,0.79159,0.61052,-129.36,0.47237,0.5478,-0.69049,254.3
> view matrix models
> #236,-0.16658,-0.56618,-0.80728,733.71,-0.98446,0.049393,0.16849,478.79,-0.055524,0.8228,-0.56561,287.22
> view matrix models
> #236,0.4492,-0.45163,-0.77088,519.64,-0.80916,-0.57146,-0.13671,694.91,-0.37879,0.68517,-0.62214,432.45
> view matrix models
> #236,0.65993,-0.46974,-0.58638,407.54,-0.74905,-0.47202,-0.46488,754.94,-0.058416,0.74602,-0.66336,339.76
> view matrix models
> #236,0.53079,-0.4452,-0.72115,479.45,-0.83669,-0.41075,-0.36226,730.28,-0.13493,0.79566,-0.59052,324.57
> view matrix models
> #236,0.35401,-0.88851,0.29195,328.65,-0.68389,-0.033001,0.72884,240.28,-0.63794,-0.45768,-0.61932,813.79
> view matrix models
> #236,0.42906,-0.90235,0.040822,390.9,-0.42585,-0.16222,0.89013,152.48,-0.79659,-0.3993,-0.45387,789.83
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.42906,-0.90235,0.040822,224.14,-0.42585,-0.16222,0.89013,22.814,-0.79659,-0.3993,-0.45387,720.65
> view matrix models
> #236,0.42906,-0.90235,0.040822,264.42,-0.42585,-0.16222,0.89013,-12.91,-0.79659,-0.3993,-0.45387,709.48
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.35817,-0.93201,-0.055435,322.64,-0.41443,-0.21191,0.88507,-1.0118,-0.83664,-0.29403,-0.46215,694.69
> view matrix models
> #236,0.67931,-0.62117,-0.39075,254.89,-0.16273,-0.64672,0.74516,91.098,-0.71558,-0.44261,-0.54041,726.03
> view matrix models
> #236,0.71295,-0.55192,-0.43253,239.94,-0.10993,-0.69717,0.70842,101.7,-0.69254,-0.45753,-0.55772,729.13
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.71295,-0.55192,-0.43253,297.54,-0.10993,-0.69717,0.70842,100.6,-0.69254,-0.45753,-0.55772,732.73
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68046,-0.63817,-0.36017,307.11,0.13892,-0.37025,0.91849,-123.81,-0.7195,-0.67503,-0.16328,674.54
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68046,-0.63817,-0.36017,294.76,0.13892,-0.37025,0.91849,-125.98,-0.7195,-0.67503,-0.16328,621.96
> view matrix models
> #236,0.68046,-0.63817,-0.36017,302.19,0.13892,-0.37025,0.91849,-125.89,-0.7195,-0.67503,-0.16328,622.96
> view matrix models
> #236,0.68046,-0.63817,-0.36017,303.09,0.13892,-0.37025,0.91849,-124.21,-0.7195,-0.67503,-0.16328,623.52
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68673,-0.57216,-0.44837,311.32,0.2108,-0.43355,0.87613,-113.66,-0.69568,-0.69618,-0.17711,627
> view matrix models
> #236,0.6869,-0.56458,-0.45762,312.14,0.21863,-0.43999,0.87099,-112.46,-0.69308,-0.69833,-0.1788,627.39
> view matrix models
> #236,0.68383,-0.61388,-0.39437,306.37,0.16624,-0.39519,0.90343,-120.29,-0.71045,-0.68336,-0.16819,624.81
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68383,-0.61388,-0.39437,314.45,0.16624,-0.39519,0.90343,-114.46,-0.71045,-0.68336,-0.16819,626.72
> view matrix models
> #236,0.68383,-0.61388,-0.39437,313.59,0.16624,-0.39519,0.90343,-113.76,-0.71045,-0.68336,-0.16819,626.96
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68659,-0.57615,-0.44344,318.1,0.20666,-0.4301,0.87881,-107.76,-0.69705,-0.69503,-0.17624,628.94
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68659,-0.57615,-0.44344,327.07,0.20666,-0.4301,0.87881,-108.47,-0.69705,-0.69503,-0.17624,628.68
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.63818,-0.60887,-0.47118,358.2,0.24341,-0.42105,0.87377,-119.57,-0.7304,-0.67231,-0.1205,614.18
> view matrix models
> #236,0.63577,-0.5548,-0.53665,364.9,0.29495,-0.46787,0.83313,-108.37,-0.7133,-0.68796,-0.13382,617.88
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.63577,-0.5548,-0.53665,372.36,0.29495,-0.46787,0.83313,-107.39,-0.7133,-0.68796,-0.13382,618.18
> hide #!234 models
> hide #!233 models
> show #!233 models
> color #233 #b2b2b2ff models
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> volume #236 step 1
> volume #236 level 0.1732
> volume #236 color #009193
[Repeated 1 time(s)]
> select add #236
2 models selected
> view matrix models
> #236,0.63577,-0.5548,-0.53665,371.67,0.29495,-0.46787,0.83313,-109.23,-0.7133,-0.68796,-0.13382,606.22
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.64925,-0.56021,-0.51443,362.37,0.19972,-0.52706,0.82603,-64.458,-0.73388,-0.63904,-0.23031,629.16
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.64925,-0.56021,-0.51443,360.82,0.19972,-0.52706,0.82603,-64.722,-0.73388,-0.63904,-0.23031,636.2
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.65709,-0.56493,-0.49909,355.08,0.13448,-0.56361,0.81502,-33.193,-0.74172,-0.60266,-0.29436,648.75
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.65709,-0.56493,-0.49909,353.84,0.13448,-0.56361,0.81502,-29.68,-0.74172,-0.60266,-0.29436,652.83
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> select add #236
2 models selected
> view matrix models
> #236,0.66843,-0.53922,-0.5123,347.9,0.2468,-0.48895,0.83667,-87.981,-0.70163,-0.68569,-0.19375,632.36
> select subtract #236
Nothing selected
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> select add #236
2 models selected
> view matrix models
> #236,0.6648,-0.54898,-0.50663,349.76,0.17003,-0.54919,0.81822,-44.49,-0.72742,-0.63009,-0.27176,649.12
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.6648,-0.54898,-0.50663,348.92,0.17003,-0.54919,0.81822,-46.742,-0.72742,-0.63009,-0.27176,656.36
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.66754,-0.54182,-0.5107,347.51,0.22647,-0.50565,0.83248,-78.738,-0.70929,-0.67138,-0.21483,644.51
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.66754,-0.54182,-0.5107,347.63,0.22647,-0.50565,0.83248,-82.762,-0.70929,-0.67138,-0.21483,639.69
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.67038,-0.53268,-0.51657,346.22,0.29731,-0.44502,0.84473,-122.74,-0.67985,-0.71987,-0.13996,620.98
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.67038,-0.53268,-0.51657,347.56,0.29731,-0.44502,0.84473,-116.97,-0.67985,-0.71987,-0.13996,611.3
> select subtract #236
Nothing selected
> select add #236
2 models selected
> view matrix models
> #236,0.67038,-0.53268,-0.51657,347.92,0.29731,-0.44502,0.84473,-119.74,-0.67985,-0.71987,-0.13996,610.38
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> select add #236
2 models selected
> view matrix models
> #236,0.67038,-0.53268,-0.51657,348.46,0.29731,-0.44502,0.84473,-117.4,-0.67985,-0.71987,-0.13996,603.72
> select subtract #236
Nothing selected
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> select add #236
2 models selected
> view matrix models
> #236,0.66305,-0.53587,-0.5227,353.3,0.32847,-0.41917,0.84641,-133.6,-0.67266,-0.7329,-0.10191,593.24
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.66305,-0.53587,-0.5227,353.67,0.32847,-0.41917,0.84641,-133.02,-0.67266,-0.7329,-0.10191,590.06
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68404,-0.53709,-0.49359,338.97,0.31215,-0.39604,0.86355,-140.12,-0.65928,-0.74477,-0.10325,589.96
> view matrix models
> #236,0.68758,-0.51714,-0.50971,337.68,0.32634,-0.40699,0.85315,-137.85,-0.64864,-0.75294,-0.11107,591.67
> view matrix models
> #236,0.68393,-0.51897,-0.51275,340.15,0.34156,-0.39327,0.85363,-145.94,-0.64466,-0.75895,-0.091709,586.07
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> show #!235 models
> hide #!235 models
> ui tool show Matchmaker
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!234 models
> select #234/C,G
1691 atoms, 1700 bonds, 2 pseudobonds, 231 residues, 2 models selected
> color (#!234 & sel) light gray
> select clear
> select #234/D,H
1488 atoms, 1494 bonds, 1 pseudobond, 203 residues, 2 models selected
> color (#!234 & sel) dim gray
> select clear
> show #!236 models
> hide #!236 models
> show #!233 models
> hide #!233 models
> show #!235 models
> hide #!235 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> color #233 #b2b2b2cb models
> color #233 #b2b2b2be models
> color #233 #b2b2b2c0 models
> color #233 #b2b2b2bf models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
[Repeated 6 time(s)]
> color #233 #b2b2b2ed models
> color #233 #b2b2b2ff models
> lighting soft
> show #!236 models
> select add #236
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68393,-0.51897,-0.51275,340.34,0.34156,-0.39327,0.85363,-144.79,-0.64466,-0.75895,-0.091709,589.32
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> ui mousemode right zoom
> hide #!233 models
> hide #!236 models
> show #!98 models
> show #!99 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> hide #!129 models
> hide #!130 models
> show #!98 models
> show #!99 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> hide #!98 models
> hide #!99 models
> show #!173 models
> volume flip #173
Opened cryosparc_P17_J858_007_volume_map.mrc z flip as #238, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map.mrc
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 4, values float32
> volume #239 step 1
> show #!173 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> hide #!173 models
> show #!173 models
> hide #!173 models
> show #!173 models
> hide #!173 models
> show #!173 models
> hide #!173 models
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #240, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!240 models
> show #!240 models
> show #!239 models
> hide #!239 models
> hide #!240 models
> show #!240 models
> close #238
> volume #240 level 0.1562
> hide #!240 models
> show #!240 models
> select add #240
2 models selected
> select subtract #240
Nothing selected
> view #240 clip false
No displayed objects specified.
> show #!237 models
> hide #!237 models
> close #237
> hide #!240 models
> show #!240 models
> close #240
> show #!239 models
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #237, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!237 models
> show #!237 models
> show #!233 models
> hide #!233 models
> hide #!237 models
> show #!237 models
> close #237
> show #!233 models
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc
> models #233
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!235 models
> show #!236 models
> show #!234 models
> hide #!234 models
> show #!233 models
> hide #!233 models
> hide #!235 models
> hide #!236 models
> show #!235 models
> hide #!235 models
> show #!235 models
> close #235
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!235 models
> show #!235 models
> close #235
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
\u2014\u2014\u2014 End of log from Thu Jul 18 17:16:17 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!236 models
> hide #!236 models
> show #!233 models
> show #!236 models
> hide #!236 models
> hide #!233 models
> show #!239 models
> lighting simple
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
> models #235
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
[Repeated 1 time(s)]
\u2014\u2014\u2014 End of log from Thu Jul 18 19:11:33 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!236 models
> hide #!236 models
> hide #!235 models
> show #!236 models
> show #!233 models
> hide #!236 models
> hide #!233 models
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_0.pdb
Chain information for ranked_0.pdb #237
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_1.pdb
Chain information for ranked_1.pdb #238
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_2.pdb
Chain information for ranked_2.pdb #240
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_3.pdb
Chain information for ranked_3.pdb #241
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_4.pdb
Chain information for ranked_4.pdb #242
---
Chain | Description
A | No description available
B C D | No description available
> hide #237 models
> show #237 models
> view #237 clip false
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!235 models
> hide #!235 models
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> cofr sel
> select subtract #237
Nothing selected
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> select subtract #237
Nothing selected
> hide #238 models
> hide #240 models
> hide #241 models
> hide #242 models
> show #238 models
> hide #238 models
> show #238 models
> hide #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #240 models
> ui tool show Matchmaker
> hide #240 models
> show #237 models
> hide #237 models
> show #!211 models
> select add #211
2 models selected
> cofr sel
> view sel
> select subtract #211
Nothing selected
> show #!221 models
> hide #!221 models
> show #!177 models
> hide #!177 models
> show #!191 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> show #!197 models
> hide #!197 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!198 models
> hide #!191 models
> show #!191 models
> select add #191
2 models selected
> select subtract #191
Nothing selected
> select add #211
2 models selected
Drag select of 211 cryosparc_P17_J843_008_volume_map_sharp.mrc
> ui mousemode right "translate selected models"
> select #211
2 models selected
> view matrix models #211,1,0,0,23.591,0,1,0,56.577,0,0,1,-51.52
> view matrix models #211,1,0,0,22.768,0,1,0,47.717,0,0,1,-59.573
> ui tool show "Fit in Map"
> fitmap #211 inMap #191
Fit map cryosparc_P17_J843_008_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map_sharp.mrc using 95383 points
correlation = 0.8844, correlation about mean = 0.6114, overlap = 1.144e+05
steps = 204, shift = 6.18, angle = 0.216 degrees
Position of cryosparc_P17_J843_008_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
Matrix rotation and translation
0.99999559 -0.00221335 -0.00198223 26.85415332
0.00221794 0.99999485 0.00231772 45.03607037
0.00197709 -0.00232210 0.99999535 -64.65124874
Axis -0.61542026 -0.52516117 0.58776156
Axis point 0.00000000 -8050.27859560 -1735.24699520
Rotation angle (degrees) 0.21598457
Shift along axis -78.17730413
> select subtract #211
Nothing selected
> hide #!191 models
> show #!191 models
> ui mousemode right zoom
[Repeated 1 time(s)]
> lighting soft
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> hide #!198 models
> hide #!211 models
> show #!190 models
> show #!226 models
> hide #!226 models
> show #!226 models
> color #226 #9437ffff models
> lighting simple
> hide #!190 models
> show #!190 models
> select add #226
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #226,-0.69587,-0.71701,-0.040702,705.69,-0.14519,0.19596,-0.9698,554.35,0.70334,-0.66895,-0.24047,350.03
> view matrix models
> #226,-0.55466,-0.80613,-0.20617,738.49,-0.80542,0.58236,-0.11025,383.62,0.20894,0.1049,-0.97229,500.26
> view matrix models
> #226,-0.93544,-0.34201,0.089373,633.42,-0.33939,0.93964,0.043527,102.84,-0.098865,0.010385,-0.99505,623.13
> ui mousemode right "translate selected models"
> view matrix models
> #226,-0.93544,-0.34201,0.089373,607.14,-0.33939,0.93964,0.043527,107.99,-0.098865,0.010385,-0.99505,615.3
> view matrix models
> #226,-0.93544,-0.34201,0.089373,604.94,-0.33939,0.93964,0.043527,90.344,-0.098865,0.010385,-0.99505,582.38
> ui mousemode right "rotate selected models"
> view matrix models
> #226,-0.92949,-0.35318,0.10634,601.2,-0.35497,0.93487,0.0022278,108.57,-0.1002,-0.035677,-0.99433,595.25
> ui mousemode right "translate selected models"
> view matrix models
> #226,-0.92949,-0.35318,0.10634,600.67,-0.35497,0.93487,0.0022278,112.16,-0.1002,-0.035677,-0.99433,599.08
> view matrix models
> #226,-0.92949,-0.35318,0.10634,604.71,-0.35497,0.93487,0.0022278,115.64,-0.1002,-0.035677,-0.99433,597.23
> fitmap #226 inMap #190
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 488089 points
correlation = 0.9693, correlation about mean = 0.8115, overlap = 1.318e+05
steps = 208, shift = 8.45, angle = 11.9 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#226) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97649779 -0.20178090 0.07573987 585.60429131
-0.21091477 0.96696460 -0.14315876 117.19127531
-0.04435107 -0.15576887 -0.98679737 611.32765515
Axis -0.10413305 0.99169911 -0.07542663
Axis point 308.30518170 0.00000000 301.15926555
Rotation angle (degrees) 176.52872801
Shift along axis 9.12733602
> select subtract #226
Nothing selected
> hide #!190 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!190 models
> hide #!226 models
> show #!230 models
> show #!231 models
> select add #230
2 models selected
> select add #231
4 models selected
> view matrix models
> #230,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596,#231,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69,#231,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1,#231,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62,#231,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24,#231,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06,#231,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44,#231,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44
> view matrix models
> #230,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44,#231,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1,#231,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1
> view matrix models
> #230,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31,#231,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01,#231,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01
> fitmap #230 inMap #190
Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 572767 points
correlation = 0.9702, correlation about mean = 0.8247, overlap = 1.352e+05
steps = 108, shift = 7.64, angle = 5.67 degrees
Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#230) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97635603 -0.20284331 0.07472287 586.20276261
-0.21174871 0.96698095 -0.14181092 117.11563644
-0.04349020 -0.15428042 -0.98706949 610.85909501
Axis -0.10460810 0.99170348 -0.07470851
Axis point 308.47483717 0.00000000 301.01098483
Rotation angle (degrees) 176.58308850
Shift along axis 9.18605482
> fitmap #231 inMap #190
Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 570393 points
correlation = 0.9715, correlation about mean = 0.8289, overlap = 1.331e+05
steps = 120, shift = 7.62, angle = 5.66 degrees
Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97634464 -0.20282850 0.07491170 586.12671435
-0.21175571 0.96700450 -0.14163978 117.05949264
-0.04371137 -0.15415222 -0.98707974 610.90239310
Axis -0.10460616 0.99170937 -0.07463300
Axis point 308.46618437 0.00000000 300.99661437
Rotation angle (degrees) 176.57124371
Shift along axis 9.18305466
> select subtract #231
2 models selected
> select subtract #230
Nothing selected
> hide #!231 models
> show #!231 models
> hide #!231 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!177 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> view matrix models #177,1,0,0,79.796,0,1,0,51.72,0,0,1,-8.0933
> ui mousemode right "rotate selected models"
> view matrix models
> #177,0.69184,0.051639,0.7202,1.2453,0.39268,0.81013,-0.4353,88.033,-0.60594,0.58396,0.54021,85.465
> view matrix models
> #177,0.68848,0.040322,0.72414,3.3706,0.40239,0.80944,-0.42765,84.826,-0.60339,0.58581,0.54106,84.445
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.68848,0.040322,0.72414,-24.721,0.40239,0.80944,-0.42765,124.91,-0.60339,0.58581,0.54106,181.95
> fitmap #177 inMap #190
Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map.mrc (#190)
using 118220 atoms
average map value = 0.2974, steps = 296
shifted from previous position = 36.4
rotated from previous position = 17.9 degrees
atoms outside contour = 74597, contour level = 0.30132
Position of 6skl (#177) relative to cryosparc_P17_J803_005_volume_map.mrc
(#190) coordinates:
Matrix rotation and translation
0.46579535 -0.09937691 0.87929456 48.24974596
0.51662113 0.83728469 -0.17904461 61.91426409
-0.71842697 0.53766029 0.44134352 233.27290342
Axis 0.38609415 0.86070423 0.33184263
Axis point 168.02643327 0.00000000 112.77870008
Rotation angle (degrees) 68.14791182
Shift along axis 149.32870821
> select subtract #177
Nothing selected
> ui mousemode right zoom
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> hide (#!177 & sel) target a
> cartoon (#!177 & sel)
> select subtract #177
Nothing selected
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!191 models
> hide #!177 models
> show #!177 models
> fitmap #177 inMap #191
Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map_sharp.mrc
(#191) using 118220 atoms
average map value = 0.3767, steps = 56
shifted from previous position = 0.0922
rotated from previous position = 0.0581 degrees
atoms outside contour = 80226, contour level = 0.39
Position of 6skl (#177) relative to
cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
Matrix rotation and translation
0.46578087 -0.09837126 0.87941531 48.10212088
0.51628561 0.83733279 -0.17978591 62.07532586
-0.71867751 0.53777030 0.44080126 233.33404225
Axis 0.38651030 0.86080969 0.33108377
Axis point 168.00088480 0.00000000 112.96763857
Rotation angle (degrees) 68.16361025
Shift along axis 149.28012082
> hide #!177 models
> show #!177 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
> show #237 models
> hide #237 models
> show #237 models
> matchmaker #237/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_0.pdb, chain B (#237), sequence
alignment score = 2258
RMSD between 412 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.877)
> hide #237 models
> show #237 models
> show #238 models
> matchmaker #238/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_1.pdb, chain B (#238), sequence
alignment score = 2254.4
RMSD between 411 pruned atom pairs is 0.626 angstroms; (across all 425 pairs:
0.888)
> matchmaker #240/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain B (#240), sequence
alignment score = 2264.6
RMSD between 414 pruned atom pairs is 0.635 angstroms; (across all 425 pairs:
0.838)
> show #240 models
> hide #240 models
> hide #237 models
> hide #238 models
> show #240 models
> hide #!177 models
> matchmaker #240/C to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain C (#240), sequence
alignment score = 2261.6
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 425 pairs:
0.840)
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #240 models
> show #241 models
> matchmaker #242/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_4.pdb, chain B (#242), sequence
alignment score = 2243.6
RMSD between 412 pruned atom pairs is 0.623 angstroms; (across all 425 pairs:
0.828)
> show #242 models
> matchmaker #241/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_3.pdb, chain B (#241), sequence
alignment score = 2265.2
RMSD between 410 pruned atom pairs is 0.661 angstroms; (across all 425 pairs:
0.961)
> hide #242 models
> hide #241 models
> show #242 models
> hide #242 models
> show #241 models
> show #242 models
> hide #241 models
> hide #242 models
> show #237 models
> hide #!177 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!177 models
> hide #!177 models
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> select #237/B#238/B#240/B#241/B#242/B
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> ui tool show "Color Actions"
> color sel lime green
> select #237/C#238/C#240/C#241/C#242/C
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> color sel lime green
> select #237/D#238/D#240/D#241/D#242/D
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> color sel lime green
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> show #!177 models
> color sel medium blue
> color sel dark blue
> color sel medium blue
[Repeated 1 time(s)]
> color sel purple
> color sel blue
> color sel medium blue
[Repeated 1 time(s)]
> select clear
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #238 models
> hide #238 models
> show #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #238 models
> show #238 models
> hide #238 models
> show #238 models
> hide #238 models
> hide #237 models
> show #240 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #240 models
> show #240 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #240 models
> show #241 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> show #242 models
> hide #242 models
> show #242 models
> hide #241 models
> show #241 models
> hide #241 models
> show #241 models
> hide #242 models
> show #237 models
> hide #237 models
> show #237 models
> hide #241 models
> show #241 models
> hide #241 models
> show #241 models
> hide #237 models
> hide #241 models
> show #237 models
> hide #237 models
> show #238 models
> show #237 models
> hide #238 models
> show #238 models
> hide #237 models
> hide #238 models
> show #240 models
> show #237 models
> hide #237 models
> hide #240 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #!239 models
> hide #!239 models
> show #240 models
> hide #240 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #237 models
> ui tool show "Show Sequence Viewer"
> sequence chain #237/A
Alignment identifier is 237/A
> select #237/A:746
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #237/A:746-757
193 atoms, 193 bonds, 12 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 193 atom styles
> style sel sphere
Changed 193 atom styles
> style sel ball
Changed 193 atom styles
> select ~sel & ##selected
38920 atoms, 39296 bonds, 2455 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel royal blue
> select clear
> show #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #238 models
> show #240 models
> show #237 models
> hide #240 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> hide #!177 models
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> select subtract #237
Nothing selected
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> show sel target ab
> hide sel target a
> cartoon sel
> ui tool show "Show Sequence Viewer"
> sequence chain #237/A
Alignment identifier is 237/A
> select subtract #237
Nothing selected
> select #237/A:746-747
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #237/A:746-757
193 atoms, 193 bonds, 12 residues, 1 model selected
> select #237/A:744
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #237/A:744-759
254 atoms, 255 bonds, 16 residues, 1 model selected
> show sel target ab
> combine #237
> hide #237 models
> show #237 models
> hide #243 models
> select #237/A:743
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #237/A:1-743
11627 atoms, 11702 bonds, 743 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #237/A:761
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #237/A:761-1096
5405 atoms, 5441 bonds, 336 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #237/A:744
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #237/A
274 atoms, 276 bonds, 17 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 274 atom styles
> select clear
> show #!211 models
> lighting soft
> color #211 #ffffb27e models
> color #211 #ffffb2c3 models
> color #211 #ffffb2ad models
> color #211 #ffffb29d models
> color #211 #ffffb28e models
> color #211 #ffffb28f models
> lighting full
> lighting simple
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes true
> color #211 #ffffb2b0 models
> color #211 #ffffb2d5 models
> color #211 #ffffb2ec models
> color #211 #ffffb2ca models
> color #211 #ffffb227 models
> color #211 #ffffb290 models
> color #211 #ffffb2b1 models
> color #211 #ffffb282 models
> color #211 #ffffb2ff models
> lighting soft
> volume #211 level 0.6913
> volume #211 level 0.65
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> show #!231 models
> hide #!230 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> color #231 #b2ffb2d9 models
> color #231 #b2ffb2c1 models
> color #231 #b2ffb2a3 models
> color #231 #b2ffb27f models
> color #231 #b2ffb26e models
> color #231 #b2ffb2ff models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> set bgColor black
> set bgColor transparent
> ui tool show "Fit in Map"
> show #243 models
> hide #243 models
> show #237 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #237 inMap #231
Fit molecule ranked_0.pdb (#237) to map
cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) using 22081 atoms
average map value = 0.3487, steps = 116
shifted from previous position = 1.47
rotated from previous position = 1.84 degrees
atoms outside contour = 10270, contour level = 0.3
Position of ranked_0.pdb (#237) relative to
cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) coordinates:
Matrix rotation and translation
0.07105997 -0.95640246 -0.28327514 285.99602561
0.71998545 0.24572901 -0.64902865 297.83602531
0.69034152 -0.15783402 0.70605736 373.36846355
Axis 0.24561334 -0.48684010 0.83824865
Axis point -161.36898166 394.59093851 0.00000000
Rotation angle (degrees) 89.34548655
Shift along axis 238.22153124
> hide #237 models
> show #237 models
> color #231 #b2ffb283 models
> set bgColor white
> set bgColor #ffffff00
> color #231 #b2ffb282 models
> color #231 #b2ffb292 models
> color #231 #b2ffb2ae models
> color #231 #b2ffb2bd models
> color #231 #b2ffb295 models
> lighting full
> lighting simple
> color #231 #b2ffb2ff models
> color #231 #b2ffb29d models
> color #231 #b2ffb2d4 models
> color #231 #b2ffb2af models
> color #231 #b2ffb2ff models
> lighting soft
> lighting full
> lighting soft
> hide #237 models
> set bgColor black
> set bgColor transparent
> hide #!231 models
> show #!230 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!226 models
> hide #!230 models
> show #!231 models
> hide #!226 models
> hide #!231 models
> show #!211 models
> show #!232 models
> hide #!232 models
> hide #!211 models
> show #!235 models
> hide #!235 models
> show #!233 models
> show #!232 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!232 models
> show #!232 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!236 models
> hide #!232 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> select add #233
2 models selected
> cofr sel
> select subtract #233
Nothing selected
> show #!236 models
> show #!232 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!231 models
> hide #!231 models
> show #!230 models
> hide #!230 models
> show #!231 models
> hide #!231 models
> hide #!236 models
> show #!236 models
> show #!234 models
> hide #!234 models
> hide #!236 models
> color #233 #b2b2b2b0 models
> hide #!233 models
> hide #!232 models
> show #!191 models
> hide #!191 models
> show #!211 models
> hide #!211 models
> show #!231 models
> show #!177 models
> hide #!177 models
> show #237 models
> hide #237 models
> hide #!231 models
> show #!233 models
> color #233 #b2b2b2ff models
> show #!236 models
> hide #!236 models
> show #!236 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Refine3D/job814/run_class001.mrc
Opened run_class001.mrc as #244, grid size 588,588,588, pixel 0.95, shown at
level 0.00486, step 4, values float32
> close #244
> hide #!236 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> lighting full
> show #!236 models
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
\u2014\u2014\u2014 End of log from Wed Jul 24 16:21:27 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!236 models
> hide #!233 models
> show #!98 models
> lighting simple
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!34 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!74 models
> show #!75 models
> hide #!75 models
> hide #!74 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!122 models
> show #!129 models
> hide #!122 models
> show #!122 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!122 models
> show #!122 models
> hide #!129 models
> show #!123 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> show #!124 models
> hide #!124 models
> show #!122 models
> hide #!122 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> hide #!123 models
> show #!123 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!123 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> show #!32 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!112 models
> hide #!112 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!110 models
> hide #!111 models
> hide #!32 models
> hide #!34 models
> show #!123 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!123 models
> show #!123 models
> hide #!122 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> hide #!130 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> lighting simple
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #244 step 1
> volume #244 level 0.344
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J685_007_volume_map.mrc
Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
pixel 1.9, shown at level 0.361, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J690_006_volume_map.mrc
Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #245 step 1
> volume #245 level 0.3413
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #246 step 1
> show #!245 models
> hide #!245 models
> show #!245 models
> select add #245
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.24392,0.87788,0.4121,-128.61,0.92708,-0.086349,-0.36479,125.94,-0.28466,0.47103,-0.83493,401.32
> view matrix models
> #245,0.64106,-0.054068,-0.76558,302.83,0.031113,-0.99486,0.096313,510.77,-0.76686,-0.085561,-0.63609,638.94
> view matrix models
> #245,0.9162,-0.026949,-0.39982,128.81,0.14241,-0.91071,0.38773,385.27,-0.37456,-0.41217,-0.83055,665.84
> view matrix models
> #245,0.91682,-0.37423,-0.13924,159.29,-0.35009,-0.92108,0.17043,579.11,-0.19203,-0.1075,-0.97548,567.39
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.91682,-0.37423,-0.13924,163.24,-0.35009,-0.92108,0.17043,567.35,-0.19203,-0.1075,-0.97548,639.7
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.98493,-0.05987,-0.16227,64.254,-0.032068,-0.98512,0.16883,496.24,-0.16996,-0.16108,-0.9722,647.31
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.98493,-0.05987,-0.16227,72.788,-0.032068,-0.98512,0.16883,503.81,-0.16996,-0.16108,-0.9722,638.94
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.96022,0.026881,-0.27794,84.445,0.064645,-0.98972,0.12761,488.12,-0.27165,-0.1405,-0.95208,656.85
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.96845,0.06341,-0.24101,63.142,0.079191,-0.99527,0.056358,503.03,-0.23629,-0.073665,-0.96889,632.88
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.96845,0.06341,-0.24101,55.646,0.079191,-0.99527,0.056358,515.43,-0.23629,-0.073665,-0.96889,633.64
> select subtract #245
Nothing selected
> hide #!245 models
> show #!246 models
> select add #246
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #246,-0.94249,-0.14738,0.29999,492.53,0.01794,-0.91854,-0.39491,640.24,0.33376,-0.36682,0.86836,47.073
> view matrix models
> #246,-0.98683,-0.012271,0.16129,511.21,-0.0067172,-0.99315,-0.11666,581.14,0.16162,-0.11621,0.97999,-7.5123
> view matrix models
> #246,-0.99462,-0.028395,0.099663,536.91,0.012491,-0.98757,-0.15671,586.65,0.10287,-0.15462,0.9826,18.639
> select subtract #246
Nothing selected
> select add #246
2 models selected
> select subtract #246
Nothing selected
> show #!245 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #245 inMap #244
Fit map cryosparc_P17_J685_007_volume_map.mrc in map
cryosparc_P17_J368_007_volume_map.mrc using 271515 points
correlation = 0.9949, correlation about mean = 0.9457, overlap = 9.464e+04
steps = 188, shift = 2.56, angle = 15.2 degrees
Position of cryosparc_P17_J685_007_volume_map.mrc (#245) relative to
cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
Matrix rotation and translation
0.99981329 -0.01923951 0.00179460 4.69427957
-0.01931352 -0.99208863 0.12404490 525.91853508
-0.00060616 -0.12405640 -0.99227498 588.72614471
Axis -0.99995314 0.00967608 -0.00029828
Axis point 0.00000000 281.31245766 277.98752927
Rotation angle (degrees) 172.87372921
Shift along axis 0.21916772
> fitmap #246 inMap #244
Fit map cryosparc_P17_J690_006_volume_map.mrc in map
cryosparc_P17_J368_007_volume_map.mrc using 254434 points
correlation = 0.9952, correlation about mean = 0.9446, overlap = 9.256e+04
steps = 120, shift = 8.54, angle = 6.45 degrees
Position of cryosparc_P17_J690_006_volume_map.mrc (#246) relative to
cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
Matrix rotation and translation
-0.99997157 0.00691924 -0.00299642 557.81739805
-0.00648161 -0.99184550 -0.12728119 593.36152310
-0.00385267 -0.12725815 0.99186215 38.74337635
Axis 0.00171577 0.06376541 -0.99796344
Axis point 279.94000643 296.98029450 0.00000000
Rotation angle (degrees) 179.61530751
Shift along axis 0.12855455
> hide #!246 models
> hide #!244 models
> show #!246 models
> ui mousemode right zoom
> lighting soft
> hide #!245 models
> show #!245 models
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!245 models
> show #!245 models
> hide #!246 models
> hide #!245 models
> show #!244 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!244 models
> hide #!244 models
> show #!244 models
> volume #244 level 0.36
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!244 models
> hide #!244 models
> show #!244 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!245 models
> show #!244 models
> hide #!246 models
> hide #!245 models
> show #!245 models
> volume #245 level 0.36
> hide #!244 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!245 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J697_006_volume_map.mrc
Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J712_007_volume_map.mrc
Opened cryosparc_P17_J712_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.349, step 2, values float32
> hide #!246 models
> show #!246 models
> hide #!246 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #247 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #248 step 1
> volume #247 level 0.36
> volume #248 level 0.36
> close #248
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J362_007_volume_map.mrc
Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.368, step 2, values float32
> hide #!247 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #248 step 1
> volume #248 level 0.36
> show #!244 models
> hide #!248 models
> show #!248 models
> hide #!244 models
> show #!244 models
> hide #!248 models
> show #!248 models
> hide #!244 models
> hide #!248 models
> show #!248 models
> show #!246 models
> show #!247 models
> hide #!247 models
> hide #!248 models
> show #!248 models
> hide #!248 models
> show #!248 models
> hide #!246 models
> show #!246 models
> hide #!248 models
> hide #!246 models
> show #!98 models
> show #!110 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!34 models
> hide #!32 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!110 models
> show #!111 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!219 models
> show #!220 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!34 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #219 step 1
> volume #220 level 0.35
> volume #219 level 0.35
> volume #219 step 2
> volume #219 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #220 step 2
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1103_006_volume_map.mrc
Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1105_008_volume_map.mrc
Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
pixel 1.9, shown at level 0.362, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1106_006_volume_map.mrc
Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
pixel 1.9, shown at level 0.357, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1107_006_volume_map.mrc
Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 2, values float32
> hide #!219 models
> hide #!220 models
> hide #!249 models
> hide #!250 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #251 step 1
> volume #251 level 0.3333
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #252 step 1
> volume #252 level 0.33
> volume #252 level 0.35
> volume #252 level 0.34
> hide #!252 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!99 models
> show #!98 models
> hide #!99 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!246 models
> hide #!246 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
\u2014\u2014\u2014 End of log from Tue Jul 30 11:34:25 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!232 models
> hide #!232 models
> show #!234 models
> show #!236 models
> lighting simple
> close #1-18
> close #22-27,32-75
> close #98-135
> close #85-90
> show #!244 models
> hide #!244 models
> close #244-252
> show #!19 models
> hide #!19 models
> open 8XGC fromDatabase pdb format mmcif
8xgc title:
Structure of yeast replisome associated with FACT and histone hexamer,
Composite map [more info...]
Chain information for 8xgc #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
8 | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
9 | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
M | FACT complex subunit POB3 | POB3_YEAST 1-552
N R | Histone H3 | A0A6A5Q536_YEASX 1-136
O S | Histone H4 | H4_YEAST 1-103
P | Histone H2A.1 | H2A1_YEAST 1-132
Q | Histone H2B.2 | H2B2_YEAST 1-131
X | DNA (51-MER) |
Y | DNA (39-MER) |
Non-standard residues in 8xgc #1
---
ADP \u2014 adenosine-5'-diphosphate
ZN \u2014 zinc ion
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,47.645,0,1,0,-186.91,0,0,1,-225.38
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.58597,0.26748,0.76491,-77.764,-0.68071,0.6746,0.28556,-31.019,-0.43963,-0.68802,0.57737,101.42
> view matrix models
> #1,-0.63049,-0.77581,0.02448,555.31,-0.40378,0.30088,-0.86396,224.99,0.66291,-0.5546,-0.50296,59.311
> view matrix models
> #1,-0.60522,-0.79563,-0.026037,564.5,-0.4515,0.37002,-0.81194,209.77,0.65563,-0.47965,-0.58317,61.313
> view matrix models
> #1,-0.51594,-0.8087,-0.28251,600.78,-0.65671,0.58517,-0.47573,138.81,0.55003,-0.059923,-0.83299,45.531
> view matrix models
> #1,-0.75431,-0.62553,0.19933,513.87,-0.20404,-0.065216,-0.97679,283.54,0.62401,-0.77747,-0.078442,28.164
> view matrix models
> #1,0.75405,0.27605,-0.59599,163.26,0.6559,-0.26853,0.70547,-200.8,0.034703,-0.92287,-0.38355,247.17
> view matrix models
> #1,0.73033,0.35167,-0.58562,150.07,0.68309,-0.37214,0.62842,-168.74,0.0030683,-0.85898,-0.51201,266.6
> view matrix models
> #1,0.72602,0.36576,-0.58233,147.32,0.68766,-0.39043,0.61212,-162.48,-0.0034657,-0.84486,-0.53498,269.69
> select subtract #1
Nothing selected
> show #!177 models
> hide #!177 models
> show #!177 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.46578,-0.098371,0.87942,92.221,0.51629,0.83733,-0.17979,-43.763,-0.71868,0.53777,0.4408,171.47
> ui mousemode right "rotate selected models"
> view matrix models
> #177,-0.49891,-0.69823,-0.51339,651.92,-0.83168,0.55231,0.057061,237.03,0.24371,0.45544,-0.85626,230.01
> view matrix models
> #177,0.26698,-0.55614,-0.78704,521.35,-0.5875,0.55345,-0.59037,305.23,0.76392,0.62,-0.17897,-27.896
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.26698,-0.55614,-0.78704,529.97,-0.5875,0.55345,-0.59037,261.16,0.76392,0.62,-0.17897,-91.066
> view matrix models
> #177,0.26698,-0.55614,-0.78704,447.11,-0.5875,0.55345,-0.59037,192.81,0.76392,0.62,-0.17897,-38.287
> select subtract #177
Nothing selected
> ui tool show "Fit in Map"
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> fitmap #177 inMap #236
Fit molecule 6skl (#177) to map cryosparc_P17_J544_007_volume_map_zflip.mrc
(#236) using 118220 atoms
average map value = 0.2679, steps = 436
shifted from previous position = 21.5
rotated from previous position = 40.5 degrees
atoms outside contour = 24734, contour level = 0.17324
Position of 6skl (#177) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.51563097 -0.12952906 -0.84696336 558.27691744
-0.84526058 -0.08486257 0.52757265 364.76426350
-0.14021148 0.98793753 -0.06572804 118.82779302
Axis 0.41616323 -0.63889353 -0.64701099
Axis point 390.84775709 -13.99098898 0.00000000
Rotation angle (degrees) 146.41962992
Shift along axis -77.59409021
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> show #!232 models
> hide #!234 models
> show #!233 models
> hide #!236 models
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #1/E to #177/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain E (#177) with 8xgc, chain E (#1), sequence alignment
score = 3091.5
RMSD between 562 pruned atom pairs is 0.577 angstroms; (across all 562 pairs:
0.577)
> hide #!233 models
> hide #!232 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> cartoon style (#!177 & sel) modeHelix tube sides 20
> select subtract #177
Nothing selected
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> matchmaker #!1 to #177
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> matchmaker #1/I to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!177 models
> show #!177 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #237 models
> hide #237 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> show #237 models
> show #!234 models
> hide #!234 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> combine #237
> hide #237 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> hide #2 models
> close #2
> open /Users/cvetkom/Documents/AlphaFold/yCsm3_Tof1_Oliver/yCsm3Tof1_AF.pdb
Chain information for yCsm3Tof1_AF.pdb #2
---
Chain | Description
A | No description available
B | No description available
> select add #2
24908 atoms, 25142 bonds, 1555 residues, 1 model selected
> view sel
> select clear
> matchmaker #2/A to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with yCsm3Tof1_AF.pdb, chain A (#2), sequence
alignment score = 5355
RMSD between 517 pruned atom pairs is 1.040 angstroms; (across all 665 pairs:
2.956)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:612
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:612-643
528 atoms, 528 bonds, 32 residues, 1 model selected
> select #2/A:612-613
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #2/A:613-657
731 atoms, 731 bonds, 45 residues, 1 model selected
> color sel blue
> color sel orange red
> select clear
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #!236 models
> hide #!236 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.0283, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_EMReady.mrc
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1207_map_sharp.mrc
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1210_map_sharp.mrc
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1163_006_volume_map.mrc
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 4, values float32
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #2 models
> show #!236 models
> show #!9 models
> volume #9 step 1
> select add #9
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,44.079,0,1,0,-129.91,0,0,1,33.561
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.89241,-0.2853,-0.34957,745.33,-0.22047,0.95166,-0.21387,0.58537,0.39369,-0.11379,-0.91217,447.06
> view matrix models
> #9,-0.86115,-0.40726,-0.30424,765.4,-0.37668,0.9131,-0.15612,41.487,0.34138,-0.019841,-0.93972,437.48
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.86115,-0.40726,-0.30424,699.37,-0.37668,0.9131,-0.15612,-44.304,0.34138,-0.019841,-0.93972,339.64
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.93636,-0.11772,-0.33072,631.45,-0.22073,0.93,0.2939,-206.54,0.27297,0.34819,-0.8968,226.48
> ui mousemode right zoom
> fitmap #9 inMap #236
Fit map cryosparc_P17_J864_007_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028136 points
correlation = 0.9937, correlation about mean = 0.9426, overlap = 1.458e+05
steps = 468, shift = 23.6, angle = 33.5 degrees
Position of cryosparc_P17_J864_007_volume_map_zflip.mrc (#9) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96823974 -0.24332681 -0.05747924 633.07873275
0.10233189 -0.59543288 0.79686125 204.91238326
-0.22812274 0.76567078 0.60142188 -52.82098481
Axis -0.08064861 0.44122957 0.89376298
Axis point 302.77781545 150.02897929 0.00000000
Rotation angle (degrees) 168.85032375
Shift along axis -7.85295761
> select subtract #9
Nothing selected
> show #!8 models
> volume #8 step 1
> select add #8
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83981,0.16349,-0.51768,159.04,-0.33783,0.90383,-0.26259,201.97,0.42496,0.39542,0.81428,-171.03
> view matrix models
> #8,-0.088093,0.71527,-0.69328,321.17,0.1227,0.69847,0.70504,-168.1,0.98853,-0.022959,-0.1493,82.529
> view matrix models
> #8,0.18202,-0.63889,-0.74746,635.26,0.31514,-0.68216,0.65981,172.32,-0.93143,-0.35565,0.077172,642.94
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.18202,-0.63889,-0.74746,569.25,0.31514,-0.68216,0.65981,-13.259,-0.93143,-0.35565,0.077172,525.18
> view matrix models
> #8,0.18202,-0.63889,-0.74746,562.71,0.31514,-0.68216,0.65981,-14.599,-0.93143,-0.35565,0.077172,487.95
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.49045,-0.55087,-0.67528,429.78,0.60915,-0.33743,0.71769,-209.84,-0.62321,-0.76334,0.17007,485.31
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.49045,-0.55087,-0.67528,444.24,0.60915,-0.33743,0.71769,-178.89,-0.62321,-0.76334,0.17007,497.07
> fitmap #8 inMap #236
Fit map cryosparc_P17_J1163_006_volume_map.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2031120 points
correlation = 0.9907, correlation about mean = 0.9161, overlap = 1.477e+05
steps = 368, shift = 21.9, angle = 21.5 degrees
Position of cryosparc_P17_J1163_006_volume_map.mrc (#8) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
0.99949009 -0.03184645 0.00231562 7.34723952
0.03147411 0.99482700 0.09658474 -35.10247418
-0.00537952 -0.09646261 0.99532207 32.64947374
Axis -0.94951030 0.03784884 0.31144447
Axis point 0.00000000 313.97495420 380.98360453
Rotation angle (degrees) 5.83455364
Shift along axis 1.86363064
> select add #8
4 models selected
> select subtract #8
Nothing selected
> lighting soft
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 silver models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J959_008_volume_map_zflip.mrc
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
> select add #10
3 models selected
> view matrix models #10,1,0,0,23.505,0,1,0,-15.929,0,0,1,-23.739
> lighting simple
> view matrix models #10,1,0,0,124.8,0,1,0,-99.812,0,0,1,-122.71
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.42765,0.3857,-0.81752,672.45,0.75258,-0.34906,-0.55837,194.61,-0.50073,-0.85404,-0.141,572.88
> view matrix models
> #10,-0.5836,0.78463,0.2092,308.37,-0.51615,-0.15955,-0.84151,586.63,-0.62689,-0.59908,0.4981,352.72
> view matrix models
> #10,-0.66506,0.6951,0.273,334.38,-0.54368,-0.20005,-0.8151,596.53,-0.51196,-0.69052,0.51096,339.61
> view matrix models
> #10,-0.87025,-0.14082,0.47205,540.96,-0.24214,-0.71221,-0.65888,593.45,0.42898,-0.68769,0.58571,53.595
> view matrix models
> #10,-0.51532,-0.60142,0.61052,515.4,0.36144,-0.79846,-0.48148,393.16,0.77704,-0.027449,0.62885,-221.63
> view matrix models
> #10,-0.57269,-0.31806,0.75556,417.1,0.29571,-0.93976,-0.17146,353.87,0.76458,0.12523,0.63225,-257.33
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.57269,-0.31806,0.75556,316.03,0.29571,-0.93976,-0.17146,301.69,0.76458,0.12523,0.63225,-291.73
> view matrix models
> #10,-0.57269,-0.31806,0.75556,307.58,0.29571,-0.93976,-0.17146,309.28,0.76458,0.12523,0.63225,-267.22
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.69988,-0.20741,0.68348,337.07,0.084924,-0.97429,-0.2087,387.97,0.70919,-0.088019,0.6995,-218.61
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.69988,-0.20741,0.68348,322.79,0.084924,-0.97429,-0.2087,374.73,0.70919,-0.088019,0.6995,-205.24
> volume #10 step 1
> fitmap #10 inMap #236
Fit map cryosparc_P17_J959_008_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028921 points
correlation = 0.9436, correlation about mean = 0.7528, overlap = 1.329e+05
steps = 224, shift = 12.9, angle = 13.2 degrees
Position of cryosparc_P17_J959_008_volume_map_zflip.mrc (#10) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96431898 -0.25440259 0.07326822 606.33395084
-0.22036646 0.61794867 -0.75470396 377.39307444
0.14672264 -0.74392121 -0.65196143 620.81486733
Axis 0.13202542 -0.89938569 0.41674293
Axis point 323.81378637 0.00000000 404.72898510
Rotation angle (degrees) 177.65962530
Shift along axis -0.65022839
> select add #10
4 models selected
> select subtract #10
Nothing selected
> color #10 #945200ff models
> color #10 #941100ff models
> color #10 #945200ff models
> color #10 #ff9300ff models
> color #10 #ff2600ff models
> color #10 #ff7e79ff models
> color #10 #fffc79ff models
> color #10 #d4fb79ff models
> color #10 #fffc79ff models
> color #10 #d4fb79ff models
> volume #10 level 0.1697
> volume #10 level 0.1731
> ui mousemode right zoom
> lighting soft
> hide #!10 models
> show #!10 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job802_run_class001.mrc
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 4, values float32
> lighting simple
> select add #11
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-51.74,0,1,0,-84.314,0,0,1,-73.541
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.0036933,-0.45538,0.89029,72.314,-0.79632,0.53717,0.27807,170.48,-0.60486,-0.70998,-0.36065,684.31
> view matrix models
> #11,-0.90602,-0.026747,0.4224,361.01,-0.42311,0.032534,-0.90549,549.65,0.010478,-0.99911,-0.040793,487.81
> view matrix models
> #11,-0.90163,0.38295,-0.20102,445.5,0.0063584,-0.453,-0.89149,546.69,-0.43245,-0.80508,0.406,428.35
> view matrix models
> #11,-0.68901,-0.48447,0.53903,379.58,0.2377,-0.85366,-0.46343,452.94,0.68467,-0.19118,0.70333,-127.8
> view matrix models
> #11,-0.70406,-0.10147,0.70285,238.48,-0.37448,-0.78789,-0.48887,615.54,0.60338,-0.60739,0.51673,55.46
> view matrix models
> #11,-0.76623,0.05272,0.6404,236.16,-0.49162,-0.68984,-0.53144,636.65,0.41376,-0.72204,0.5545,125.83
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.76623,0.05272,0.6404,261.62,-0.49162,-0.68984,-0.53144,557.66,0.41376,-0.72204,0.5545,116.13
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.60221,0.45689,0.65467,110.25,-0.62773,-0.77766,-0.034707,467.75,0.49325,-0.43186,0.75511,-39.317
> view matrix models
> #11,-0.68577,0.26569,0.67759,174.57,-0.57475,-0.76886,-0.28021,524.85,0.44652,-0.58161,0.67996,33.93
> volume #11 step 1
> fitmap #11 inMap #236
Fit map Ref3D_job802_run_class001.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2030281 points
correlation = 0.9571, correlation about mean = 0.8205, overlap = 3535
steps = 488, shift = 19.8, angle = 32.9 degrees
Position of Ref3D_job802_run_class001.mrc (#11) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96450343 -0.25313673 0.07519943 605.61171904
-0.21928378 0.60909585 -0.76217904 383.34466562
0.14713185 -0.75161431 -0.64298380 621.67767309
Axis 0.13173116 -0.89692214 0.42211086
Axis point 323.99781428 0.00000000 407.81801536
Rotation angle (degrees) 177.70184669
Shift along axis -1.63548244
> hide #!10 models
> select add #11
4 models selected
> select subtract #11
Nothing selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!233 models
> show #!3 models
> volume #3 step 1
> volume #3 level 0.2689
> hide #!3 models
> show #!3 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> fitmap #3 inMap #233
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc using 171797 points
correlation = 0.9986, correlation about mean = 0.9835, overlap = 1.873e+05
steps = 64, shift = 2.32, angle = 0.05 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc (#233) coordinates:
Matrix rotation and translation
0.99999969 -0.00055856 -0.00055446 0.28221116
0.00055877 0.99999977 0.00037517 -0.20830704
0.00055425 -0.00037548 0.99999978 -2.35151229
Axis -0.43044636 -0.63576954 0.64071291
Axis point 2074.34448759 -648.53479123 0.00000000
Rotation angle (degrees) 0.04995831
Shift along axis -1.49568576
> volume #3 level 0.25
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!234 models
> hide #!236 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!232 models
> show #!234 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> select add #234
18238 atoms, 19000 bonds, 223 pseudobonds, 1946 residues, 5 models selected
> view matrix models
> #232,-0.019001,-0.99844,0.052579,192.68,-0.84729,0.043998,0.5293,242.41,-0.53078,-0.034493,-0.84681,167.29,#234,-0.045299,-0.99887,-0.014131,189.08,-0.79838,0.027697,0.60152,244.8,-0.60045,0.03853,-0.79874,172.18
> ui mousemode right "translate selected models"
> view matrix models
> #232,-0.019001,-0.99844,0.052579,192.71,-0.84729,0.043998,0.5293,242.76,-0.53078,-0.034493,-0.84681,167.34,#234,-0.045299,-0.99887,-0.014131,189.11,-0.79838,0.027697,0.60152,245.15,-0.60045,0.03853,-0.79874,172.22
> select subtract #234
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> select subtract #232
Nothing selected
> hide #!234 models
> show #!234 models
> hide #!232 models
> hide #!234 models
> volume flip #4,5,6
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at step 1, values float32
> hide #!13 models
> volume #12 level 0.6868
> hide #!14 models
> volume #12 level 1.994
> volume #12 level 2.112
> hide #!12 models
> show #!13 models
> volume #13 level 0.04456
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!13 models
> show #!14 models
> volume #14 level 0.06454
> volume #14 level 0.1669
> hide #!14 models
> show #!14 models
> volume #14 level 0.2071
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!7 models
> volume #7 level 0.1489
> volume #7 step 1
> volume #7 level 0.2483
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #7
3 models selected
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95557,0.0046513,-0.29472,69.933,0.27535,0.34272,0.89818,-107.26,0.10519,-0.93943,0.32621,316.27
> view matrix models
> #7,0.91915,0.11688,-0.37617,70.997,0.39267,-0.1961,0.89853,-18.651,0.031252,-0.97359,-0.22614,454.39
> view matrix models
> #7,0.91426,0.13556,-0.38178,69.268,0.40482,-0.26848,0.87409,-0.87336,0.015992,-0.9537,-0.30034,468.92
> view matrix models
> #7,0.95579,-0.038803,-0.29149,78.32,0.26406,-0.32299,0.90882,32.378,-0.12941,-0.94561,-0.29846,496.89
> view matrix models
> #7,0.94972,0.029908,-0.31167,69.398,0.30564,-0.30453,0.90213,21.312,-0.067931,-0.95203,-0.29836,485.5
> view matrix models
> #7,0.9488,-0.094559,-0.30141,93.528,0.2555,-0.33137,0.90825,36.024,-0.18576,-0.93875,-0.29025,505.38
> view matrix models
> #7,0.95015,-0.094376,-0.29717,92.323,0.25152,-0.33129,0.90939,36.591,-0.18427,-0.9388,-0.29104,505.25
> view matrix models
> #7,0.95804,-0.094732,-0.27054,85.191,0.22599,-0.33099,0.91617,40.384,-0.17634,-0.93887,-0.29569,504.6
> view matrix models
> #7,0.9581,-0.19453,-0.21025,93.469,0.13432,-0.34319,0.92961,59.077,-0.25299,-0.9189,-0.30268,517.72
> view matrix models
> #7,0.95765,-0.21305,-0.19368,93.974,0.11202,-0.34399,0.93227,63.299,-0.26525,-0.91448,-0.30556,519.93
> hide #!3 models
> show #!3 models
> view matrix models
> #7,0.95696,-0.21706,-0.19263,94.734,0.10944,-0.34484,0.93226,64.012,-0.26878,-0.91322,-0.30625,520.54
> view matrix models
> #7,0.94815,-0.27392,-0.1612,101.89,0.14424,-0.081125,0.98621,-9.7554,-0.28322,-0.95833,-0.03741,476.68
> view matrix models
> #7,0.95414,-0.24037,-0.17843,97.229,0.16379,-0.079738,0.98327,-13.471,-0.25057,-0.9674,-0.036713,471.68
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.95414,-0.24037,-0.17843,96.447,0.16379,-0.079738,0.98327,-14.654,-0.25057,-0.9674,-0.036713,467.78
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99024,-0.071411,-0.11966,41.263,0.11264,-0.095331,0.98905,-2.0232,-0.082036,-0.99288,-0.086357,448.67
> view matrix models
> #7,0.99499,-0.013505,-0.099097,23.84,0.096797,-0.11921,0.98814,6.4479,-0.025158,-0.99278,-0.1173,443.37
> view matrix models
> #7,0.996,0.01454,-0.088107,15.449,0.089245,-0.12802,0.98775,9.9368,0.0030827,-0.99167,-0.1288,439.71
> view matrix models
> #7,0.99258,0.11362,-0.043338,-13.986,0.055935,-0.11014,0.99234,12.115,0.10798,-0.9874,-0.11568,414.38
> view matrix models
> #7,0.99638,0.054238,-0.065393,2.2931,0.06993,-0.086471,0.9938,3.9549,0.048247,-0.99478,-0.089951,422.89
> select subtract #7
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> fitmap #7 inMap #3
Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
steps = 140, shift = 3.54, angle = 8.85 degrees
Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99817702 -0.04588002 0.03921297 3.35030958
-0.04066443 -0.03114210 0.99868743 12.39857491
-0.04459863 -0.99846141 -0.03295101 431.82063884
Axis -0.99911720 0.04192858 0.00260921
Axis point 0.00000000 215.36415158 209.87663468
Rotation angle (degrees) 91.88869867
Shift along axis -1.70078525
> fitmap #7 inMap #3
Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
steps = 52, shift = 0.00236, angle = 0.00447 degrees
Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99817611 -0.04587745 0.03923922 3.34208981
-0.04068728 -0.03106753 0.99868882 12.38761501
-0.04459824 -0.99846385 -0.03287749 431.80589646
Axis -0.99911670 0.04194141 0.00259649
Axis point 0.00000000 215.36687767 209.87412872
Rotation angle (degrees) 91.88448023
Shift along axis -1.69840331
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> lighting soft
> lighting full
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> volume #7 level 0.22
> lighting simple
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!3 models
> close #144-146,148-154
> show #!162 models
> hide #!162 models
> close #162-165
> close #169-171
> show #!12 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> volume #13 level 0.04
> volume #13 level 0.02
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!14 models
> hide #!13 models
> volume #14 level 0.25
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!14 models
> hide #!11 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> show #2 models
> hide #2 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/I
Alignment identifier is 1/I
> select #1/I:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> color sel red
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #1
Nothing selected
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!19 models
> hide #!19 models
> close
> #19-21,76-84,91-97,136-140,142-143,155-156,158-159,161,166-168,172-173,175-176
> show #!178 models
> hide #!178 models
> show #!232 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> hide #!234 models
> show #!233 models
> hide #!233 models
> close #180-231
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> color #9 #d6d6d6ff models
> color #9 silver models
> color #9 darkgrey models
> color #9 #919191ff models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #2 models
> hide #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> show #!3 models
> select add #8
3 models selected
> select subtract #8
Nothing selected
> select add #8
3 models selected
> ui tool show "Color Actions"
> color sel light sea green
> select subtract #8
Nothing selected
> hide #!8 models
> show #!9 models
> select add #9
2 models selected
> color sel steel blue
> select subtract #9
Nothing selected
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #!3 models
> fitmap #13 inMap #3
Fit map cryosparc_P17_J1207_map_sharp.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 135754 points
correlation = 0.8195, correlation about mean = 0.6657, overlap = 1.259e+04
steps = 52, shift = 2.26, angle = 0.101 degrees
Position of cryosparc_P17_J1207_map_sharp.mrc z flip (#13) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99999956 -0.00066700 -0.00066264 0.29074301
0.00066701 0.99999978 0.00001245 -0.17783395
0.00066263 -0.00001289 0.99999978 -0.07194977
Axis -0.01347599 -0.70471591 0.70936161
Axis point 192.41646705 437.19131956 0.00000000
Rotation angle (degrees) 0.05387447
Shift along axis 0.07036596
> hide #!13 models
> show #!12 models
> fitmap #12 inMap #3
Fit map cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 178682 points
correlation = 0.9651, correlation about mean = 0.6584, overlap = 2.725e+05
steps = 56, shift = 2.37, angle = 0.0731 degrees
Position of cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip (#12)
relative to cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999939 0.00102607 0.00041428 -0.30090785
-0.00102640 0.99999915 0.00080313 0.12472239
-0.00041345 -0.00080355 0.99999959 0.19980920
Axis -0.58749376 0.30266385 -0.75049695
Axis point 102.26087289 256.35146195 0.00000000
Rotation angle (degrees) 0.07834647
Shift along axis 0.06457425
> hide #!12 models
> fitmap #14 inMap #3
Fit map cryosparc_P17_J1210_map_sharp.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 113255 points
correlation = 0.9486, correlation about mean = 0.6387, overlap = 2.633e+04
steps = 52, shift = 2.43, angle = 0.0525 degrees
Position of cryosparc_P17_J1210_map_sharp.mrc z flip (#14) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99999995 0.00019277 -0.00024648 0.02840578
-0.00019280 0.99999997 -0.00012225 0.02141418
0.00024646 0.00012230 0.99999996 -0.18912634
Axis 0.36395622 -0.73365042 -0.57384051
Axis point 527.18097402 0.00000000 -37.18039835
Rotation angle (degrees) 0.01924876
Shift along axis 0.10315629
> show #!14 models
> hide #!14 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!8 models
> hide #!11 models
> hide #2 models
> hide #!3 models
> show #!11 models
> show #!7 models
> combine #7
No structures specified
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
> volume #15 step 1
> volume #15 level 0.22
> select add #15
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,100.39,0,1,0,-46.513,0,0,1,45.903
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.80976,-0.45265,0.37335,153.4,0.3286,0.877,0.35057,-163.14,-0.48611,-0.1612,0.8589,208.93
> view matrix models
> #15,0.48179,-0.6745,0.5594,227.28,0.3403,0.73229,0.58987,-186.41,-0.80751,-0.093832,0.58234,319.83
> view matrix models
> #15,0.11088,-0.79909,0.5909,322.74,0.17639,0.60095,0.77958,-165.65,-0.97805,0.017785,0.20759,411.17
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.11088,-0.79909,0.5909,326.79,0.17639,0.60095,0.77958,-133.13,-0.97805,0.017785,0.20759,331.85
> view matrix models
> #15,0.11088,-0.79909,0.5909,305.76,0.17639,0.60095,0.77958,-140.24,-0.97805,0.017785,0.20759,332.58
> view matrix models
> #15,0.11088,-0.79909,0.5909,312.36,0.17639,0.60095,0.77958,-53.435,-0.97805,0.017785,0.20759,338.76
> view matrix models
> #15,0.11088,-0.79909,0.5909,308.51,0.17639,0.60095,0.77958,-56.402,-0.97805,0.017785,0.20759,338.76
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.024164,-0.79613,0.60464,332.95,0.20877,0.58746,0.78186,-60.832,-0.97767,0.14512,0.15201,324.44
> view matrix models
> #15,-0.11821,-0.78529,0.60774,349.54,0.18703,0.58347,0.7903,-57.299,-0.97522,0.20709,0.077898,326.9
> view matrix models
> #15,-0.105,-0.78677,0.60825,347,0.20205,0.58199,0.78769,-59.555,-0.97373,0.2056,0.097857,322.7
> view matrix models
> #15,-0.19293,-0.90299,-0.3839,597.45,0.097707,-0.40698,0.90819,138.04,-0.97633,0.13771,0.16675,322.58
> view matrix models
> #15,-0.14742,-0.90868,-0.3906,590.6,0.015659,-0.39701,0.91768,150.99,-0.98895,0.12916,0.072754,346.69
> view matrix models
> #15,-0.22245,-0.89505,-0.38653,602.49,0.048703,-0.40617,0.9125,147.11,-0.97373,0.18416,0.13394,319.48
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,572.78,0.083751,-0.20657,0.97484,86.116,-0.97098,0.20301,0.12644,316.65
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,576.09,0.083751,-0.20657,0.97484,-0.31383,-0.97098,0.20301,0.12644,309.91
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,576.03,0.083751,-0.20657,0.97484,0.10503,-0.97098,0.20301,0.12644,306.13
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.2138,-0.95931,-0.18443,574.53,0.10809,-0.21087,0.97152,-3.3553,-0.97088,0.18777,0.14877,304.52
> view matrix models
> #15,-0.23097,-0.97294,-0.0055806,543.26,0.1557,-0.042623,0.98688,-50.688,-0.96042,0.22707,0.16133,291.71
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.23097,-0.97294,-0.0055806,539.65,0.1557,-0.042623,0.98688,-54.918,-0.96042,0.22707,0.16133,290.53
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.28101,-0.95968,0.0065516,544.75,0.21102,-0.055129,0.97593,-61.509,-0.93622,0.27563,0.21801,263.72
> hide #!15 models
> show #!15 models
> select subtract #15
Nothing selected
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!7 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> select add #15
2 models selected
> view matrix models
> #15,-0.25657,-0.95952,-0.11618,565.46,0.1776,-0.16496,0.97018,-31.028,-0.95007,0.22828,0.21274,277.33
> view matrix models
> #15,-0.2471,-0.95598,-0.15824,571.63,0.16674,-0.20281,0.96492,-19.967,-0.95454,0.21204,0.20951,282.24
> select subtract #15
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!11 models
> show #!177 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #243 models
> hide #243 models
> close #240-243
> show #!239 models
> hide #!239 models
> close #239
> close #237-238
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Tue Sep 3 13:30:10 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!3 models
> show #!3 models
> show #!232 models
> hide #!232 models
> show #!1 models
> hide #!177 models
> hide #!3 models
> hide #!15 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #20b2aa8f models
> set bgColor white
> color #8 #20b2aaa3 models
> color #8 #20b2aaab models
> color #8 #20b2aaae models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #20b2aa8a models
> show #!232 models
> hide #!8 models
> show #!8 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/L
Alignment identifier is 1/L
> select clear
> select #1/L:905-996
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> hide #!8 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> show #!1 models
> show #!8 models
> hide #!232 models
> lighting soft
> lighting full
> lighting simple
> hide #!1 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J535_003_volume_map_zflip.mrc
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.0831, step 4, values float32
> select add #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
> cofr sel
> select subtract #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> select add #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
> view sel
> select subtract #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> volume #16 step 1
> volume #16 level 0.2325
> select add #16
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 5 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.25096,-0.5068,-0.82472,635.54,0.24628,-0.85738,0.45193,125.51,-0.93614,-0.089699,0.33999,418.44,#16,0.38885,-0.060579,0.91931,48.211,-0.26865,0.94702,0.17604,66.153,-0.88126,-0.31542,0.35197,458.59
> view matrix models
> #1,-0.22215,-0.94943,-0.22187,455.62,0.42836,-0.29946,0.85254,-75.15,-0.87587,0.094354,0.47323,351.85,#16,-0.088966,0.51185,0.85446,2.4214,-0.38273,0.77443,-0.50376,264.06,-0.91957,-0.37184,0.127,524.01
> view matrix models
> #1,-0.38537,-0.9141,-0.12615,489.05,0.83574,-0.40371,0.37223,-86.716,-0.39118,0.038019,0.91953,35.134,#16,-0.26392,0.43198,0.8624,77.602,0.2312,0.89637,-0.37824,28.981,-0.93643,0.099556,-0.33645,444.31
> view matrix models
> #1,-0.1356,-0.57517,-0.80671,587.5,0.91613,-0.38283,0.11895,-42.958,-0.37725,-0.72292,0.57884,147.36,#16,0.44409,0.060297,0.89395,-3.9514,0.47456,0.83047,-0.29176,-31.753,-0.75999,0.5538,0.34018,134.84
> view matrix models
> #1,0.26845,-0.68107,-0.68124,397.8,0.89856,-0.077833,0.4319,-135.6,-0.34718,-0.72807,0.59108,132.33,#16,0.6063,0.40624,0.68364,-132.59,0.26507,0.70727,-0.65536,126.61,-0.74976,0.57856,0.32114,126.66
> view matrix models
> #1,0.38233,-0.62566,-0.67998,352.57,0.87609,0.011513,0.48201,-143.78,-0.29374,-0.78001,0.55254,124.4,#16,0.68689,0.42691,0.58816,-147.27,0.22309,0.64636,-0.72969,170.71,-0.69167,0.63243,0.34874,87.742
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.38233,-0.62566,-0.67998,380.63,0.87609,0.011513,0.48201,-254.96,-0.29374,-0.78001,0.55254,165.63,#16,0.68689,0.42691,0.58816,-119.21,0.22309,0.64636,-0.72969,59.535,-0.69167,0.63243,0.34874,128.97
> view matrix models
> #1,0.38233,-0.62566,-0.67998,289.1,0.87609,0.011513,0.48201,-274.53,-0.29374,-0.78001,0.55254,190.38,#16,0.68689,0.42691,0.58816,-210.74,0.22309,0.64636,-0.72969,39.961,-0.69167,0.63243,0.34874,153.72
> view matrix models
> #1,0.38233,-0.62566,-0.67998,298.14,0.87609,0.011513,0.48201,-272.93,-0.29374,-0.78001,0.55254,167.18,#16,0.68689,0.42691,0.58816,-201.7,0.22309,0.64636,-0.72969,41.57,-0.69167,0.63243,0.34874,130.51
> view matrix models
> #1,0.38233,-0.62566,-0.67998,282.73,0.87609,0.011513,0.48201,-276.94,-0.29374,-0.78001,0.55254,170.84,#16,0.68689,0.42691,0.58816,-217.11,0.22309,0.64636,-0.72969,37.554,-0.69167,0.63243,0.34874,134.18
> view matrix models
> #1,0.38233,-0.62566,-0.67998,281.94,0.87609,0.011513,0.48201,-275.2,-0.29374,-0.78001,0.55254,167.66,#16,0.68689,0.42691,0.58816,-217.9,0.22309,0.64636,-0.72969,39.291,-0.69167,0.63243,0.34874,130.99
> select subtract #16
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> ui tool show "Fit in Map"
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #1
Nothing selected
> fitmap #16 inMap #8
Fit map cryosparc_P17_J535_003_volume_map_zflip.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 276739 points
correlation = 0.9612, correlation about mean = 0.5525, overlap = 1.969e+04
steps = 164, shift = 2.78, angle = 15.9 degrees
Position of cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99998050 -0.00425494 -0.00457199 0.73851682
-0.00391421 -0.99738877 0.07211322 540.07003803
-0.00486689 -0.07209391 -0.99738598 573.94195717
Axis -0.99999512 0.00204496 0.00236281
Axis point 0.00000000 280.39509902 277.22388946
Rotation angle (degrees) 175.86516180
Shift along axis 1.72202130
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> fitmap #3 inMap #16
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J535_003_volume_map_zflip.mrc using 193604 points
correlation = 0.9176, correlation about mean = 0.2012, overlap = 2.042e+04
steps = 124, shift = 8.42, angle = 17.5 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) coordinates:
Matrix rotation and translation
0.58513310 0.56587388 -0.58086660 162.67581615
0.53803292 0.26503049 0.80017461 1.17881883
0.60674527 -0.78073400 -0.14938067 218.34134813
Axis -0.79945189 -0.60056511 -0.01407893
Axis point 0.00000000 55.92177713 150.33929755
Rotation angle (degrees) 98.60424165
Shift along axis -133.83346040
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #16
2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light sea green
> color sel cornflower blue
> color sel dark turquoise
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> color sel powder blue
> color sel light steel blue
> color sel pale turquoise
> color sel light blue
> color sel light sky blue
> select subtract #16
Nothing selected
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!3 models
> show #!8 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J655_005_volume_map_sharp.mrc
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.168, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #18 level 0.2742
> volume #18 step 1
> volume #18 level 0.4422
> volume #17 step 1
> volume #17 level 0.4266
> select add #17
2 models selected
> view matrix models #17,1,0,0,61.784,0,1,0,-62.478,0,0,1,-102.28
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.48945,0.25112,-0.83509,356.29,-0.79242,0.52783,-0.30572,377.6,0.36402,0.81137,0.45734,-292.7
> view matrix models
> #17,0.15791,0.038191,-0.98672,550.87,-0.45006,0.89221,-0.03749,107.36,0.87893,0.45,0.15807,-262.93
> view matrix models
> #17,-0.52223,0.57538,-0.62945,504.75,-0.48515,0.40657,0.77416,41.996,0.70136,0.70967,0.066821,-260.32
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,736.95,-0.72536,0.46156,0.5107,164.54,0.3622,0.88681,-0.28703,-119.76
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,769.33,-0.72536,0.46156,0.5107,134.03,0.3622,0.88681,-0.28703,-184.13
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,689.38,-0.72536,0.46156,0.5107,105.15,0.3622,0.88681,-0.28703,-37.942
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,631.43,-0.72536,0.46156,0.5107,-28.227,0.3622,0.88681,-0.28703,-100.2
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.3388,-0.27569,-0.89956,653.75,-0.79784,0.59094,0.11938,58.328,0.49867,0.75815,-0.42016,-69.159
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.3388,-0.27569,-0.89956,660.19,-0.79784,0.59094,0.11938,89.728,0.49867,0.75815,-0.42016,-58.912
> fitmap #17 inMap #8
Fit map cryosparc_P17_J655_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 286513 points
correlation = 0.8688, correlation about mean = 0.2449, overlap = 8.66e+04
steps = 256, shift = 11.4, angle = 20.7 degrees
Position of cryosparc_P17_J655_005_volume_map_sharp.mrc (#17) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.95262622 -0.30211083 -0.03510445 642.60145687
0.17067519 -0.62654330 0.76046925 202.72382050
-0.25174046 0.71845148 0.64842440 -51.92560179
Axis -0.08053233 0.41521020 0.90615398
Axis point 303.70069952 160.23700769 0.00000000
Rotation angle (degrees) 164.87800612
Shift along axis -14.62978716
> select subtract #17
Nothing selected
> hide #!17 models
> show #!17 models
> show #!18 models
> select add #18
2 models selected
> view matrix models #18,1,0,0,64.318,0,1,0,-54.342,0,0,1,-66.309
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.21982,0.46975,-0.85499,506.62,-0.95518,0.074469,0.28649,397.56,0.19825,0.87965,0.43233,-216.22
> view matrix models
> #18,-0.94049,0.19544,-0.278,639.01,-0.33946,-0.50251,0.79514,246.97,0.015703,0.84219,0.53895,-181.2
> view matrix models
> #18,-0.54157,-0.62412,-0.56319,821.43,-0.82771,0.27878,0.487,253.66,-0.14694,0.7299,-0.66757,207.28
> view matrix models
> #18,-0.42526,-0.61847,-0.66079,811.74,-0.90422,0.2587,0.3398,319.03,-0.039206,0.742,-0.66925,173.54
> view matrix models
> #18,-0.94737,0.13657,-0.28954,659.99,-0.1521,0.60383,0.78247,-104.74,0.2817,0.78533,-0.55128,39.326
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,734.43,-0.3217,0.63403,0.70321,-43.906,0.13504,0.76582,-0.62871,106.65
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,676.58,-0.3217,0.63403,0.70321,-192.92,0.13504,0.76582,-0.62871,39.473
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,622.9,-0.3217,0.63403,0.70321,-192.02,0.13504,0.76582,-0.62871,103.22
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.79577,-0.00053325,-0.6056,623.89,-0.55271,0.40935,0.72591,-70.483,0.24752,0.91238,-0.32605,-47.021
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.79577,-0.00053325,-0.6056,629.43,-0.55271,0.40935,0.72591,-66.36,0.24752,0.91238,-0.32605,-58.769
> fitmap #18 inMap #8
Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
correlation = 0.7365, correlation about mean = 0.04959, overlap = 5.271e+04
steps = 264, shift = 14.2, angle = 19.7 degrees
Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.98450205 -0.17536898 0.00119668 603.21178623
0.16771790 -0.93951186 0.29864389 420.47135877
-0.05124858 0.29421622 0.95436387 -43.01006329
Axis -0.01275615 0.15109534 0.98843689
Axis point 282.81965590 240.21101021 0.00000000
Rotation angle (degrees) 170.00569893
Shift along axis 13.32387113
> select subtract #18
Nothing selected
> hide #!18 models
> show #!18 models
> hide #!17 models
> select add #18
2 models selected
> view matrix models
> #18,-0.71292,0.17712,-0.6785,584.31,-0.44227,0.63729,0.63107,-109.78,0.54418,0.74999,-0.37601,-58.453
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.60845,0.16613,-0.77601,582.51,-0.56737,0.59263,0.57173,-46.453,0.55487,0.78815,-0.26633,-100.21
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,668.78,-0.55166,0.81473,0.17855,-9.9926,0.63987,0.55072,-0.53597,9.6575
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,676.27,-0.55166,0.81473,0.17855,-55.746,0.63987,0.55072,-0.53597,-8.0105
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,686.76,-0.55166,0.81473,0.17855,-55.075,0.63987,0.55072,-0.53597,-10.997
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,683.39,-0.55166,0.81473,0.17855,-62.825,0.63987,0.55072,-0.53597,-15.419
> fitmap #18 inMap #8
Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
correlation = 0.8615, correlation about mean = 0.2577, overlap = 9.246e+04
steps = 124, shift = 4.79, angle = 8.22 degrees
Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.95287653 -0.30128223 -0.03543080 642.50639609
0.16990142 -0.62678199 0.76044582 202.97462428
-0.25131620 0.71859123 0.64843413 -52.01912235
Axis -0.08049372 0.41518546 0.90616874
Axis point 303.68746244 160.20985177 0.00000000
Rotation angle (degrees) 164.93072677
Shift along axis -14.58371648
> select subtract #18
Nothing selected
> hide #!18 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> volume #19 step 1
> volume #19 level 0.3083
> volume #19 level 0.349
> ui mousemode right "rotate selected models"
> select add #19
3 models selected
> view matrix models
> #19,-0.44408,0.45825,0.76993,46.649,-0.84084,-0.50996,-0.18146,698.91,0.30948,-0.72797,0.61178,228.1
> view matrix models
> #19,0.74377,0.47854,0.4667,-198.52,-0.1168,0.7805,-0.61415,275.9,-0.65815,0.40228,0.63641,182.36
> view matrix models
> #19,0.63923,-0.27239,0.71916,-40.675,0.75039,0.42547,-0.50585,98.912,-0.16819,0.86301,0.47637,-31.378
> view matrix models
> #19,0.48406,-0.45879,0.74511,45.429,0.87025,0.16344,-0.46471,124.56,0.091425,0.87338,0.47838,-107
> view matrix models
> #19,0.42748,-0.56077,0.70909,99.683,0.84962,-0.018802,-0.52707,198.53,0.30889,0.82776,0.4684,-152.09
> view matrix models
> #19,0.34186,-0.69155,0.63631,180.84,0.90812,0.068905,-0.41301,124.28,0.24177,0.71904,0.65156,-158.63
> view matrix models
> #19,0.71424,0.27698,0.64276,-188.14,0.046489,0.89756,-0.43844,146.08,-0.69835,0.34303,0.6282,212.11
> view matrix models
> #19,0.62219,0.51419,0.59033,-211.39,-0.24699,0.84448,-0.47524,253.15,-0.74288,0.14988,0.65243,269.79
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.62219,0.51419,0.59033,-152.75,-0.24699,0.84448,-0.47524,157.57,-0.74288,0.14988,0.65243,108.45
> view matrix models
> #19,0.62219,0.51419,0.59033,-232.8,-0.24699,0.84448,-0.47524,39.083,-0.74288,0.14988,0.65243,122.29
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.80455,0.20201,0.55847,-189.06,0.21173,0.78102,-0.58752,-37.641,-0.55486,0.59094,0.58559,-30.003
> view matrix models
> #19,0.66658,0.035494,0.74459,-161.06,0.34504,0.87073,-0.3504,-170.05,-0.66077,0.49048,0.56817,31.993
> view matrix models
> #19,0.69056,-0.011725,0.72318,-148.48,0.35206,0.87887,-0.32193,-182.74,-0.63181,0.47691,0.61104,14.806
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.69056,-0.011725,0.72318,-139.38,0.35206,0.87887,-0.32193,-182.11,-0.63181,0.47691,0.61104,39.587
> fitmap #19 inMap #8
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 437476 points
correlation = 0.926, correlation about mean = 0.3771, overlap = 9.23e+04
steps = 76, shift = 5.07, angle = 2.91 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99898029 -0.04235492 0.01563476 10.76195054
-0.02350758 -0.78361084 -0.62080710 683.98076137
0.03854581 0.61980652 -0.78380744 301.98502466
Axis 0.99971420 -0.01846223 0.01518761
Axis point 0.00000000 289.57241421 269.88486029
Rotation angle (degrees) 141.64850238
Shift along axis 2.71749516
> select subtract #19
Nothing selected
> hide #!8 models
> show #!17 models
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
> volume #20 step 1
> volume #20 level 0.1747
> volume #20 level 0.2443
> volume #21 step 1
> volume #21 level 0.2884
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #20
2 models selected
> select add #21
4 models selected
> view matrix models
> #20,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669,#21,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01,#21,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01
> view matrix models
> #20,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7,#21,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7
> view matrix models
> #20,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18,#21,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18
> view matrix models
> #20,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31,#21,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335,#21,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335
> view matrix models
> #20,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993,#21,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993
> hide #!19 models
> show #!8 models
> fitmap #20 inMap #8
Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 832636 points
correlation = 0.9229, correlation about mean = 0.5258, overlap = 1.189e+05
steps = 380, shift = 9.47, angle = 18.4 degrees
Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#20) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99901244 -0.04125012 0.01650989 10.10628769
-0.02203512 -0.78263856 -0.62208628 683.70365274
0.03858241 0.62110813 -0.78277461 301.46889960
Axis 0.99972305 -0.01774976 0.01545187
Axis point 0.00000000 289.37571004 269.89498614
Rotation angle (degrees) 141.55453890
Shift along axis 2.62616910
> hide #!21 models
> show #!21 models
> fitmap #21 inMap #8
Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 615528 points
correlation = 0.9307, correlation about mean = 0.4766, overlap = 1.046e+05
steps = 256, shift = 8.97, angle = 18.4 degrees
Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#21) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99901041 -0.04132365 0.01644837 10.15187435
-0.02212851 -0.78259628 -0.62213616 683.73846275
0.03858136 0.62115652 -0.78273626 301.42350706
Axis 0.99972248 -0.01779698 0.01543467
Axis point 0.00000000 289.39631274 269.89032870
Rotation angle (degrees) 141.55091738
Shift along axis 2.63294913
> select subtract #21
2 models selected
> select subtract #20
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!19 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> volume #19 level 0.3
> volume #20 level 0.3
> volume #21 level 0.3
> ui mousemode right zoom
> lighting soft
> hide #!20 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!19 models
> show #!19 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!21 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!21 models
> show #!177 models
> hide #!19 models
> show #!19 models
> fitmap #177 inMap #19
Fit molecule 6skl (#177) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
(#19) using 118220 atoms
average map value = 0.3221, steps = 64
shifted from previous position = 0.243
rotated from previous position = 0.297 degrees
atoms outside contour = 66812, contour level = 0.3
Position of 6skl (#177) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52950222 -0.10066174 -0.84231504 552.59666642
0.51811377 0.74784553 -0.41507252 112.80308239
0.67170345 -0.65619683 -0.34383163 339.58429947
Axis -0.14584759 -0.91577637 0.37427547
Axis point 163.10260363 0.00000000 350.04343026
Rotation angle (degrees) 124.24578811
Shift along axis -56.79921564
> hide #!19 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select subtract #177
Nothing selected
> color #19 #b2b2ff80 models
> color #19 #b2b2ffb4 models
> color #19 #b2b2ffbf models
> color #19 #b2b2ffd8 models
> color #19 #b2b2ffc6 models
> color #19 #b2b2ffc7 models
> set bgColor black
> set bgColor transparent
> hide #!177 models
> show #!177 models
> color #19 #b2b2ffff models
> color #19 #b2b2fffb models
> color #19 #b2b2ffff models
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!177 models
> show #!19 models
> show #!1 models
> hide #!1 models
> show #!177 models
> hide #!177 models
> show #!15 models
> hide #!15 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> ui tool show Matchmaker
> show #!1 models
> show #!177 models
> matchmaker #1/I to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> select #1/8
6947 atoms, 7098 bonds, 7 pseudobonds, 859 residues, 3 models selected
> combine #1
> hide #!22 models
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> select #1/9
4594 atoms, 4699 bonds, 3 pseudobonds, 573 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!1 models
> set bgColor white
> set bgColor #ffffff00
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!177 models
> show #!177 models
> combine #177
[Repeated 2 time(s)]
> rename #23 6skl-Mcm2
> hide #!24 models
> hide #!25 models
> hide #!177 models
> hide #!23 models
> show #!23 models
> select #23/2
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> select ~sel & ##selected
107602 atoms, 108697 bonds, 122 pseudobonds, 6649 residues, 4 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> select add #23
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> ui tool show "Color Actions"
> color sel hot pink
> show #!19 models
> color #19 #b2b2ffea models
> color #19 #b2b2ffde models
> color #19 #b2b2ffff models
> color #19 #b2b2ffdd models
> color #19 #b2b2ffd4 models
> hide #!19 models
> show #!19 models
> color #19 #b2b2ffff models
> select subtract #23
Nothing selected
> hide #!19 models
> show #!19 models
> color #19 #b2b2ff7f models
> color #19 #b2b2ffd4 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting full
> color #19 #b2b2ff82 models
> color #19 #b2b2ff90 models
> hide #!19 models
> show #!19 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!19 models
> combine #23
> ui tool show "Show Sequence Viewer"
> sequence chain #23/2
Alignment identifier is 23/2
> select clear
[Repeated 1 time(s)]
> select #23/2:173-442
4279 atoms, 4320 bonds, 270 residues, 1 model selected
> select #23/2:458-459
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #23/2:458-459
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #23/2:458
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #23/2:173-458
4533 atoms, 4577 bonds, 286 residues, 1 model selected
> select #23/2:466-467
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #23/2:173-467
4653 atoms, 4697 bonds, 295 residues, 1 model selected
> select #23/2:465-466
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #23/2:465-466
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #23/2:465
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #23/2:173-465
4631 atoms, 4675 bonds, 293 residues, 1 model selected
> select ~sel & ##selected
5987 atoms, 6033 bonds, 8 pseudobonds, 379 residues, 3 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> hide #!26 models
> rename #23 N-Mcm2_6skl
> show #!26 models
> hide #!23 models
> ui tool show "Show Sequence Viewer"
> sequence chain #26/2
Alignment identifier is 26/2
> select #26/2:466
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #26/2:466-868
5941 atoms, 5986 bonds, 1 pseudobond, 376 residues, 2 models selected
> select ~sel & ##selected
4677 atoms, 4722 bonds, 7 pseudobonds, 296 residues, 2 models selected
> delete atoms (#!26 & sel)
> delete bonds (#!26 & sel)
> rename #26 C-Mcm2_6skl
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!26 models
> show #!24 models
> lighting simple
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!26 models
> hide #!24 models
> show #!24 models
> select #25/3
9752 atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
> select add #25
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select subtract #25
Nothing selected
> hide #!24 models
> show #!24 models
> select #24/3
9752 atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
> select ~sel & ##selected
108468 atoms, 109566 bonds, 123 pseudobonds, 6703 residues, 4 models selected
> delete atoms (#!24 & sel)
> delete bonds (#!24 & sel)
> rename #24 Mcm3_6skl
> combine #24
> ui tool show "Show Sequence Viewer"
> sequence chain #24/3
Alignment identifier is 24/3
> sequence chain #27/3
Alignment identifier is 27/3
> hide #!27 models
> select #24/3:332
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #24/3:18-332
4424 atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
> select ~sel & ##selected
5328 atoms, 5363 bonds, 6 pseudobonds, 336 residues, 3 models selected
> delete atoms (#!24 & sel)
> delete bonds (#!24 & sel)
> rename #24 N-Mcm3_6skl
> show #!27 models
> hide #!24 models
> select clear
> select #27/3:337-675
4320 atoms, 4351 bonds, 1 pseudobond, 275 residues, 2 models selected
> select clear
> select #27/3:337-740
5283 atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select ~sel & ##selected
4469 atoms, 4522 bonds, 5 pseudobonds, 284 residues, 3 models selected
> delete atoms (#!27 & sel)
> delete bonds (#!27 & sel)
> rename #27 C-Mcm3_6skl
> show #!24 models
> select add #27
5283 atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select add #24
9707 atoms, 9793 bonds, 3 pseudobonds, 616 residues, 4 models selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel cyan
[Repeated 1 time(s)]
> color sel turquoise
[Repeated 1 time(s)]
> color sel pale turquoise
[Repeated 4 time(s)]
> color sel turquoise
[Repeated 1 time(s)]
> select subtract #27
4424 atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
> select subtract #24
Nothing selected
> hide #!24 models
> hide #!27 models
> combine #177
[Repeated 1 time(s)]
> hide #!28 models
> hide #!29 models
> show #!25 models
> select #25/4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select #25/4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select ~sel & ##selected
107337 atoms, 108453 bonds, 119 pseudobonds, 6641 residues, 4 models selected
> delete atoms (#!25 & sel)
> delete bonds (#!25 & sel)
> rename #25 Mcm4_6skl
> combine #25
> ui tool show "Show Sequence Viewer"
> sequence chain #25/4
Alignment identifier is 25/4
> sequence chain #30/4
Alignment identifier is 30/4
> hide #!30 models
> select #25/4:469
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/4:174-469
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> select ~sel & ##selected
6090 atoms, 6118 bonds, 11 pseudobonds, 384 residues, 3 models selected
> delete atoms (#!25 & sel)
> delete bonds (#!25 & sel)
> rename #25 N-Mcm4_6skl
> show #!30 models
> hide #!25 models
> select clear
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select clear
> select #30/4:505-927
6089 atoms, 6118 bonds, 6 pseudobonds, 383 residues, 2 models selected
> select ~sel & ##selected
4794 atoms, 4834 bonds, 5 pseudobonds, 297 residues, 3 models selected
> delete atoms (#!30 & sel)
> delete bonds (#!30 & sel)
> rename #30 C-Mcm4_6skl
> show #!25 models
> select add #25
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> select add #30
10882 atoms, 10952 bonds, 6 pseudobonds, 679 residues, 3 models selected
> ui tool show "Color Actions"
> color sel forest green
> color sel sea green
> color sel turquoise
> color sel sea green
> color sel green
> color sel forest green
> color sel sea green
[Repeated 1 time(s)]
> select subtract #30
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> hide #!30 models
> select subtract #25
Nothing selected
> hide #!25 models
> show #!28 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> select #28/5
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select ~sel & ##selected
108498 atoms, 109616 bonds, 119 pseudobonds, 6707 residues, 4 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> rename #28 Mcm5_6skl
> combine #28
> select add #28
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select add #31
19444 atoms, 19578 bonds, 22 pseudobonds, 1228 residues, 6 models selected
> ui tool show "Color Actions"
> color sel yellow
> select subtract #28
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select subtract #31
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #28/5
Alignment identifier is 28/5
> sequence chain #31/5
Alignment identifier is 31/5
> select #28/5:342
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #28/5:20-342
4172 atoms, 4202 bonds, 4 pseudobonds, 259 residues, 2 models selected
> select ~sel & ##selected
5550 atoms, 5587 bonds, 7 pseudobonds, 355 residues, 2 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> hide #!31 models
> rename #28 N-Mcm5_6skl
> show #!25 models
> show #!30 models
> hide #!30 models
> hide #!25 models
> show #!31 models
> hide #!31 models
> hide #!28 models
> show #!31 models
> select #31/5:343
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #31/5:343-694
5504 atoms, 5540 bonds, 352 residues, 1 model selected
> select ~sel & ##selected
4218 atoms, 4249 bonds, 11 pseudobonds, 262 residues, 3 models selected
> delete atoms (#!31 & sel)
> delete bonds (#!31 & sel)
> rename #31 C-Mcm5_6skl
> show #!28 models
> hide #!28 models
> hide #!31 models
> combine #177
> hide #!32 models
> show #!29 models
> select #29/6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select #29/6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select ~sel & ##selected
108175 atoms, 109279 bonds, 121 pseudobonds, 6683 residues, 4 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> rename #29 Mcm6_6skl
> combine #29
> select add #29
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select add #33
20090 atoms, 20252 bonds, 18 pseudobonds, 1276 residues, 6 models selected
> ui tool show "Color Actions"
> color sel orange
> color sel dark orange
> color sel orange
> color sel dark orange
[Repeated 1 time(s)]
> color sel goldenrod
> color sel dark orange
> color sel sandy brown
> color sel dark orange
[Repeated 1 time(s)]
> select subtract #29
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select subtract #33
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #29/6
Alignment identifier is 29/6
> sequence chain #33/6
Alignment identifier is 33/6
> select #29/6:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #29/6:459-463
72 atoms, 71 bonds, 5 residues, 1 model selected
> select
> #29/6:98-102,105-122,134-147,155-161,164-193,277-284,384-386,407-411,500-521,524-533,540-553,580-592,604-609,626-631,640-650,652-658,694-699,702-707,720-735,747-759,766-784,796-814,820-836
4489 atoms, 4500 bonds, 275 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #29/6:91-463
4862 atoms, 4908 bonds, 2 pseudobonds, 305 residues, 2 models selected
> select ~sel & ##selected
5183 atoms, 5218 bonds, 7 pseudobonds, 333 residues, 3 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> rename #29 N-Mcm6_6skl
> hide #!29 models
> show #!29 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!28 models
> show #!31 models
> hide #!31 models
> hide #!29 models
> hide #!28 models
> show #!28 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #!28 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #!31 models
> show #!29 models
> show #!33 models
> show #!28 models
> hide #!28 models
> hide #!33 models
> show #!33 models
> hide #!29 models
> select clear
[Repeated 2 time(s)]
> select #33/6:497-838
5182 atoms, 5218 bonds, 2 pseudobonds, 332 residues, 2 models selected
> select ~sel & ##selected
4863 atoms, 4908 bonds, 7 pseudobonds, 306 residues, 3 models selected
> delete atoms (#!33 & sel)
> delete bonds (#!33 & sel)
> rename #33 C-Mcm6_6skl
> show #!29 models
> hide #!29 models
> hide #!33 models
> show #!32 models
> select #32/7
9981 atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
> select ~sel & ##selected
108239 atoms, 109350 bonds, 119 pseudobonds, 6685 residues, 4 models selected
> delete atoms (#!32 & sel)
> delete bonds (#!32 & sel)
> select add #32
9981 atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
> rename #32 Mcm7_6skl
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> select subtract #32
Nothing selected
> combine #32
> ui tool show "Show Sequence Viewer"
> sequence chain #32/7
Alignment identifier is 32/7
> sequence chain #34/7
Alignment identifier is 34/7
> ui tool show "Show Sequence Viewer"
> sequence chain #32/7
Destroying pre-existing alignment with identifier 32/7
Alignment identifier is 32/7
> sequence chain #34/7
Destroying pre-existing alignment with identifier 34/7
Alignment identifier is 34/7
> select #32/7:385
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #32/7:4-385
4942 atoms, 4986 bonds, 3 pseudobonds, 317 residues, 2 models selected
> select ~sel & ##selected
5039 atoms, 5069 bonds, 8 pseudobonds, 319 residues, 3 models selected
> delete atoms (#!32 & sel)
> delete bonds (#!32 & sel)
> rename #32 N-Mcm7_6skl
> select clear
> select #34/7:396-729
5038 atoms, 5069 bonds, 3 pseudobonds, 318 residues, 2 models selected
> select ~sel & ##selected
4943 atoms, 4986 bonds, 8 pseudobonds, 318 residues, 3 models selected
> delete atoms (#!34 & sel)
> delete bonds (#!34 & sel)
> rename #34 C-Mcm7_6skl
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> combine #177
[Repeated 3 time(s)]
> hide #!36 models
> hide #!37 models
> hide #!38 models
> hide #!35 models
> show #!23 models
> show #!24 models
> show #!25 models
> show #!26 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> show #!32 models
> show #!33 models
> show #!34 models
> hide #!34 models
> hide #!33 models
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!35 models
> select #35/E
9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
> select ~sel & ##selected
109091 atoms, 110192 bonds, 126 pseudobonds, 6757 residues, 4 models selected
> delete atoms (#!35 & sel)
> delete bonds (#!35 & sel)
> rename #35 Cdc45_6skl
> select add #35
9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light cyan
[Repeated 1 time(s)]
> color sel powder blue
> color sel light blue
[Repeated 1 time(s)]
> color sel light cyan
> select subtract #35
Nothing selected
> lighting soft
[Repeated 1 time(s)]
> lighting full
> hide #!35 models
> show #!36 models
> lighting simple
> select #36/A,B,C,D
13385 atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
> select ~sel & ##selected
104835 atoms, 105897 bonds, 124 pseudobonds, 6511 residues, 4 models selected
> delete atoms (#!36 & sel)
> delete bonds (#!36 & sel)
> select add #36
13385 atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
> rename #36 GINS_6skl
> ui tool show "Color Actions"
> color sel silver
> color sel gray
> select clear
> hide #!36 models
> show #!37 models
> select #37/F,G,H
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> select ~sel & ##selected
97999 atoms, 98929 bonds, 124 pseudobonds, 6050 residues, 4 models selected
> delete atoms (#!37 & sel)
> delete bonds (#!37 & sel)
> select add #37
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> ui tool show "Color Actions"
> color sel slate blue
> color sel medium slate blue
[Repeated 3 time(s)]
> color sel royal blue
> color sel dodger blue
> color sel royal blue
[Repeated 1 time(s)]
> color sel dodger blue
> color sel royal blue
> select subtract #37
Nothing selected
> show #!32 models
> hide #!32 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> rename #37 Ctf4_6skl
> combine #177
> hide #!39 models
> show #!38 models
> select #38/X
10990 atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
> select ~sel & ##selected
107230 atoms, 108313 bonds, 123 pseudobonds, 6656 residues, 4 models selected
> delete atoms (#!38 & sel)
> delete bonds (#!38 & sel)
> rename #38 Tof1_6skl
> select add #38
10990 atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
> ui tool show "Color Actions"
> color sel slate blue
> color sel medium slate blue
> color sel royal blue
> color sel medium slate blue
[Repeated 7 time(s)]
> color sel dark slate blue
> color sel medium slate blue
> select subtract #38
Nothing selected
> hide #!38 models
> show #!38 models
> show #!39 models
> hide #!38 models
> select #39/Y
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> select ~sel & ##selected
116604 atoms, 117773 bonds, 130 pseudobonds, 7227 residues, 4 models selected
> delete atoms (#!39 & sel)
> delete bonds (#!39 & sel)
> rename #39 Csm3_6skl
> select add #39
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> hide #!39 models
> select subtract #39
Nothing selected
> show #!39 models
> show #!38 models
> show #!37 models
> show #!36 models
> show #!35 models
> show #!34 models
> show #!33 models
> show #!32 models
> show #!31 models
> show #!30 models
> show #!29 models
> show #!28 models
> show #!27 models
> show #!26 models
> show #!25 models
> show #!24 models
> show #!23 models
> select add #39
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel blue violet
> color sel deep pink
> color sel magenta
> color sel dark magenta
> color sel purple
[Repeated 1 time(s)]
> color sel dark magenta
> color sel purple
[Repeated 1 time(s)]
> color sel medium purple
> color sel purple
[Repeated 1 time(s)]
> select subtract #39
Nothing selected
> combine #177
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!34 models
> hide #!33 models
> hide #!40 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!40 models
> select #40/I,J
1878 atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
> select ~sel & ##selected
116342 atoms, 117390 bonds, 80 pseudobonds, 7262 residues, 3 models selected
> delete atoms (#!40 & sel)
> delete bonds (#!40 & sel)
> rename #40 DNA_6skl
> select #40/I
1192 atoms, 1279 bonds, 37 residues, 1 model selected
> color sel black
> select #40/J
686 atoms, 736 bonds, 22 residues, 1 model selected
> color sel dim gray
> select clear
> hide #!40 models
> show #!19 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!19 models
> show #!24 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!23 models
> show #!19 models
> fitmap #23 inMap #19
Fit molecule N-Mcm2_6skl (#23) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
average map value = 0.4542, steps = 52
shifted from previous position = 1.09
rotated from previous position = 3.28 degrees
atoms outside contour = 1773, contour level = 0.3
Position of N-Mcm2_6skl (#23) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.48619287 -0.07981194 -0.87019915 544.75612919
0.53368692 0.76140981 -0.36801274 98.39251819
0.69194998 -0.64333907 -0.32759742 329.31388927
Axis -0.16188679 -0.91851479 0.36072599
Axis point 157.28465121 0.00000000 346.27079505
Rotation angle (degrees) 121.74840423
Shift along axis -59.77172713
> fitmap #23 inMap #19
Fit molecule N-Mcm2_6skl (#23) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
average map value = 0.4542, steps = 36
shifted from previous position = 0.0153
rotated from previous position = 0.0153 degrees
atoms outside contour = 1772, contour level = 0.3
Position of N-Mcm2_6skl (#23) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.48612668 -0.08005636 -0.87021368 544.79200838
0.53355946 0.76145094 -0.36811244 98.44034714
0.69209476 -0.64326002 -0.32744679 329.22783276
Axis -0.16176651 -0.91852227 0.36076090
Axis point 157.31175798 0.00000000 346.27934228
Rotation angle (degrees) 121.73971426
Shift along axis -59.77622153
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> fitmap #24 inMap #19
Fit molecule N-Mcm3_6skl (#24) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4424 atoms
average map value = 0.4899, steps = 72
shifted from previous position = 1.7
rotated from previous position = 1.03 degrees
atoms outside contour = 1496, contour level = 0.3
Position of N-Mcm3_6skl (#24) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51684057 -0.09904554 -0.85033277 552.53192555
0.53049272 0.74253315 -0.40892786 109.84096466
0.67190275 -0.66244585 -0.33122832 337.40029650
Axis -0.15211044 -0.91333918 0.37772207
Axis point 161.67410853 0.00000000 351.20284420
Rotation angle (degrees) 123.55710836
Shift along axis -56.92439016
> hide #!24 models
> show #!25 models
> fitmap #25 inMap #19
Fit molecule N-Mcm4_6skl (#25) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4793 atoms
average map value = 0.4529, steps = 52
shifted from previous position = 2.33
rotated from previous position = 1.94 degrees
atoms outside contour = 1614, contour level = 0.3
Position of N-Mcm4_6skl (#25) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51485483 -0.08657680 -0.85289447 549.29032703
0.51292450 0.76605243 -0.38739145 104.77742894
0.68690099 -0.63692082 -0.34999843 331.94917409
Axis -0.14931878 -0.92141613 0.35874256
Axis point 162.77097442 0.00000000 344.51466083
Rotation angle (degrees) 123.32588851
Shift along axis -59.47868024
> hide #!25 models
> show #!28 models
> fitmap #28 inMap #19
Fit molecule N-Mcm5_6skl (#28) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4172 atoms
average map value = 0.5001, steps = 48
shifted from previous position = 0.477
rotated from previous position = 0.518 degrees
atoms outside contour = 1491, contour level = 0.3
Position of N-Mcm5_6skl (#28) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52208241 -0.10009271 -0.84700143 552.10007852
0.52281543 0.74707399 -0.41054169 110.98680483
0.67386497 -0.65716201 -0.33770418 337.87117097
Axis -0.14839770 -0.91514390 0.37481963
Axis point 162.27606171 0.00000000 350.25308806
Rotation angle (degrees) 123.80418376
Shift along axis -56.85853328
> hide #!28 models
> show #!29 models
> fitmap #29 inMap #19
Fit molecule N-Mcm6_6skl (#29) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4862 atoms
average map value = 0.4386, steps = 64
shifted from previous position = 1.82
rotated from previous position = 1.81 degrees
atoms outside contour = 1794, contour level = 0.3
Position of N-Mcm6_6skl (#29) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50972104 -0.08434926 -0.85619488 547.63107126
0.52443527 0.75845239 -0.38693363 104.75971281
0.68202061 -0.64624700 -0.34236341 333.92722557
Axis -0.15485966 -0.91860876 0.36356077
Axis point 160.21705818 0.00000000 346.31455571
Rotation angle (degrees) 123.14885220
Shift along axis -59.63631555
> hide #!29 models
> show #!32 models
> fitmap #32 inMap #19
Fit molecule N-Mcm7_6skl (#32) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4942 atoms
average map value = 0.4432, steps = 72
shifted from previous position = 2.55
rotated from previous position = 2 degrees
atoms outside contour = 1716, contour level = 0.3
Position of N-Mcm7_6skl (#32) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50209844 -0.09646270 -0.85941382 551.56164113
0.52217420 0.75834411 -0.39019012 105.12547600
0.68937019 -0.64467757 -0.33039306 330.21496061
Axis -0.15084576 -0.91803150 0.36669294
Axis point 162.01873803 0.00000000 348.31963616
Rotation angle (degrees) 122.48465413
Shift along axis -58.62173799
> hide #!32 models
> show #!26 models
> hide #!26 models
> show #!27 models
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 68
shifted from previous position = 2.23
rotated from previous position = 2.57 degrees
atoms outside contour = 3746, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49125191 -0.10951013 -0.86410596 552.71575277
0.52980778 0.74986873 -0.39623302 105.24621685
0.69135757 -0.65246028 -0.31035512 328.13372850
Axis -0.15062172 -0.91437023 0.37581934
Axis point 161.23471230 0.00000000 351.59387631
Rotation angle (degrees) 121.72677225
Shift along axis -56.16600219
> hide #!27 models
> show #!26 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> fitmap #26 inMap #19
Fit molecule C-Mcm2_6skl (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
average map value = 0.2499, steps = 120
shifted from previous position = 7.11
rotated from previous position = 16.9 degrees
atoms outside contour = 4089, contour level = 0.3
Position of C-Mcm2_6skl (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.72499338 -0.17926092 -0.66501889 564.61757623
0.30570305 0.78146839 -0.54392354 172.58562424
0.61719547 -0.59763926 -0.51175880 374.68531048
Axis -0.03915385 -0.93461689 0.35349433
Axis point 195.27960459 0.00000000 339.48855257
Rotation angle (degrees) 136.68906839
Shift along axis -50.95925582
> hide #!26 models
> show #!27 models
> hide #!27 models
> show #!30 models
> hide #!30 models
> show #!31 models
> fitmap #31 inMap #19
Fit molecule C-Mcm5_6skl (#31) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5504 atoms
average map value = 0.2192, steps = 72
shifted from previous position = 1.38
rotated from previous position = 0.644 degrees
atoms outside contour = 4241, contour level = 0.3
Position of C-Mcm5_6skl (#31) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52798995 -0.11167009 -0.84187672 553.62723896
0.51297984 0.74809912 -0.42095058 113.66344352
0.67681482 -0.65412346 -0.33770431 336.54923223
Axis -0.14058346 -0.91564213 0.37661090
Axis point 164.28052383 0.00000000 350.23415639
Rotation angle (degrees) 123.97268209
Shift along axis -55.15775830
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!33 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> fitmap #33 inMap #19
Fit molecule C-Mcm6_6skl (#33) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5182 atoms
average map value = 0.2506, steps = 100
shifted from previous position = 2.49
rotated from previous position = 3.08 degrees
atoms outside contour = 3615, contour level = 0.3
Position of C-Mcm6_6skl (#33) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.56822296 -0.11833571 -0.81432140 555.66185955
0.48213507 0.75407081 -0.44600784 124.85237619
0.66683465 -0.64604479 -0.37142655 342.86696321
Axis -0.12419139 -0.91956426 0.37279763
Axis point 169.39701035 0.00000000 347.59627562
Rotation angle (degrees) 126.35519939
Shift along axis -55.99821082
> hide #!33 models
> show #!34 models
> fitmap #34 inMap #19
Fit molecule C-Mcm7_6skl (#34) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
average map value = 0.2488, steps = 84
shifted from previous position = 3.58
rotated from previous position = 6.44 degrees
atoms outside contour = 3687, contour level = 0.3
Position of C-Mcm7_6skl (#34) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.60810284 -0.04397762 -0.79263921 541.80870758
0.49024443 0.76452307 -0.41852703 112.51289532
0.62439678 -0.64309443 -0.44334887 361.42999934
Axis -0.14668479 -0.92559125 0.34894756
Axis point 166.00281620 0.00000000 336.12434083
Rotation angle (degrees) 130.05063287
Shift along axis -57.49592849
> hide #!34 models
> show #!26 models
> fitmap #26 inMap #19
Fit molecule C-Mcm2_6skl (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
average map value = 0.2499, steps = 40
shifted from previous position = 0.00827
rotated from previous position = 0.0158 degrees
atoms outside contour = 4089, contour level = 0.3
Position of C-Mcm2_6skl (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.72508101 -0.17912737 -0.66495934 564.59530186
0.30560205 0.78160601 -0.54378253 172.54320727
0.61714254 -0.59749932 -0.51198599 374.71726789
Axis -0.03915999 -0.93466297 0.35337179
Axis point 195.28291115 0.00000000 339.45035239
Rotation angle (degrees) 136.69646920
Shift along axis -50.96478166
> hide #!26 models
> show #!27 models
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 48
shifted from previous position = 0.00561
rotated from previous position = 0.0144 degrees
atoms outside contour = 3745, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49119447 -0.10962931 -0.86412349 552.72708725
0.52963562 0.75000136 -0.39621215 105.24134461
0.69153026 -0.65228780 -0.31033293 328.08057761
Axis -0.15052098 -0.91441153 0.37575921
Axis point 161.25504150 0.00000000 351.58454506
Rotation angle (degrees) 121.71962364
Shift along axis -56.15162171
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 44
shifted from previous position = 0.00644
rotated from previous position = 0.00323 degrees
atoms outside contour = 3747, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49121423 -0.10960226 -0.86411569 552.72290598
0.52966978 0.74997300 -0.39622018 105.24674287
0.69149006 -0.65232495 -0.31034441 328.08956470
Axis -0.15054136 -0.91440312 0.37577152
Axis point 161.25087455 0.00000000 351.58379235
Rotation angle (degrees) 121.72163061
Shift along axis -56.15889268
> hide #!27 models
> show #!33 models
> hide #!33 models
> show #!34 models
> fitmap #34 inMap #19
Fit molecule C-Mcm7_6skl (#34) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
average map value = 0.2488, steps = 40
shifted from previous position = 0.021
rotated from previous position = 0.0237 degrees
atoms outside contour = 3683, contour level = 0.3
Position of C-Mcm7_6skl (#34) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.60807905 -0.04366734 -0.79267461 541.74998075
0.49057375 0.76436052 -0.41843804 112.46427092
0.62416126 -0.64330876 -0.44336957 361.50164606
Axis -0.14689577 -0.92554158 0.34899056
Axis point 165.95199356 0.00000000 336.12532515
Rotation angle (degrees) 130.05660056
Shift along axis -57.51048000
> hide #!34 models
> show #!35 models
> fitmap #35 inMap #19
Fit molecule Cdc45_6skl (#35) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 9129 atoms
average map value = 0.4936, steps = 32
shifted from previous position = 0.989
rotated from previous position = 0.293 degrees
atoms outside contour = 3011, contour level = 0.3
Position of Cdc45_6skl (#35) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53238330 -0.10222439 -0.84030840 552.34452064
0.51398389 0.74970935 -0.41684104 113.43549525
0.67259838 -0.65382418 -0.34659105 340.11300103
Axis -0.14356656 -0.91653277 0.37330461
Axis point 163.36596759 0.00000000 349.77928908
Rotation angle (degrees) 124.37677529
Shift along axis -56.29979678
> hide #!35 models
> show #!36 models
> fitmap #36 inMap #19
Fit molecule GINS_6skl (#36) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 13385 atoms
average map value = 0.5009, steps = 64
shifted from previous position = 1.25
rotated from previous position = 0.693 degrees
atoms outside contour = 4520, contour level = 0.3
Position of GINS_6skl (#36) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53440728 -0.10575367 -0.83858514 554.21323619
0.51997798 0.74104668 -0.42482082 114.22988038
0.66635709 -0.66307314 -0.34103116 341.67599231
Axis -0.14464380 -0.91365555 0.37988381
Axis point 163.82286606 0.00000000 351.69409164
Rotation angle (degrees) 124.55491640
Shift along axis -54.73309110
> hide #!36 models
> show #!37 models
> fitmap #37 inMap #19
Fit molecule Ctf4_6skl (#37) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 20221 atoms
average map value = 0.3967, steps = 68
shifted from previous position = 1.75
rotated from previous position = 0.685 degrees
atoms outside contour = 7725, contour level = 0.3
Position of Ctf4_6skl (#37) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53679956 -0.10566869 -0.83706653 554.09013415
0.51701361 0.74282869 -0.42532631 116.11912844
0.66674070 -0.66108976 -0.34411796 343.05037030
Axis -0.14335492 -0.91438332 0.37861921
Axis point 163.58631600 0.00000000 352.06583111
Rotation angle (degrees) 124.68361653
Shift along axis -55.72348034
> hide #!37 models
> show #!38 models
> fitmap #38 inMap #19
Fit molecule Tof1_6skl (#38) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 10990 atoms
average map value = 0.3486, steps = 52
shifted from previous position = 2.71
rotated from previous position = 2.1 degrees
atoms outside contour = 4840, contour level = 0.3
Position of Tof1_6skl (#38) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50884095 -0.07790103 -0.85732860 546.87430545
0.52700003 0.75928729 -0.38177714 104.30156172
0.68069954 -0.64607604 -0.34530262 334.50800166
Axis -0.15791244 -0.91893600 0.36141430
Axis point 159.52485154 0.00000000 345.83620169
Rotation angle (degrees) 123.19075103
Shift along axis -61.30873983
> hide #!38 models
> show #!39 models
> fitmap #39 inMap #19
Fit molecule Csm3_6skl (#39) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 1616 atoms
average map value = 0.3779, steps = 60
shifted from previous position = 2.5
rotated from previous position = 1.9 degrees
atoms outside contour = 645, contour level = 0.3
Position of Csm3_6skl (#39) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51530602 -0.07349129 -0.85384937 547.02376900
0.53880358 0.74699785 -0.38946748 106.53379719
0.66644611 -0.66075203 -0.34533512 340.04339220
Axis -0.16330007 -0.91514372 0.36857164
Axis point 158.27460801 0.00000000 348.00938205
Rotation angle (degrees) 123.83627701
Shift along axis -61.49240111
> hide #!39 models
> show #!40 models
> fitmap #40 inMap #19
Fit molecule DNA_6skl (#40) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
(#19) using 1878 atoms
average map value = 0.3403, steps = 80
shifted from previous position = 1.35
rotated from previous position = 3.78 degrees
atoms outside contour = 831, contour level = 0.3
Position of DNA_6skl (#40) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.47993510 -0.10126507 -0.87144001 550.20291579
0.51412450 0.77241029 -0.37290528 101.33591686
0.71087151 -0.62699899 -0.31864396 321.37532285
Axis -0.14801492 -0.92172967 0.35847734
Axis point 161.49135847 0.00000000 346.98780116
Rotation angle (degrees) 120.86949809
Shift along axis -59.63678931
> hide #!40 models
> show #!40 models
> hide #!40 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> combine #23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40
Remapping chain ID '2' in C-Mcm2_6skl #26 to '5'
Remapping chain ID '3' in C-Mcm3_6skl #27 to '6'
Remapping chain ID '5' in N-Mcm5_6skl #28 to '7'
Remapping chain ID '6' in N-Mcm6_6skl #29 to '8'
Remapping chain ID '4' in C-Mcm4_6skl #30 to '9'
Remapping chain ID '5' in C-Mcm5_6skl #31 to '0'
Remapping chain ID '7' in N-Mcm7_6skl #32 to 'AA'
Remapping chain ID '6' in C-Mcm6_6skl #33 to 'AB'
Remapping chain ID '7' in C-Mcm7_6skl #34 to 'AC'
> hide #!19 models
> select add #41
118080 atoms, 119265 bonds, 97 pseudobonds, 7310 residues, 3 models selected
> cartoon style (#!41 & sel) xsection oval modeHelix default
> cartoon style (#!41 & sel) xsection rectangle modeHelix default
> cartoon style (#!41 & sel & coil) xsection oval
> cartoon style (#!41 & sel) xsection barbell modeHelix default
> cartoon style (#!41 & sel) xsection oval modeHelix default
> cartoon hide (#!41 & sel)
> show (#!41 & sel) target ab
> ui tool show "Color Zone"
> select subtract #41
Nothing selected
> hide #!41 models
> show #!19 models
> color #19 #b2b2ffff models
> volume copy #19
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!42 models
> show #!42 models
> show #!41 models
> hide #!41 models
> ui tool show "Hide Dust"
> surface dust #42 size 5.7
> surface dust #42 size 5.67
> surface dust #42 size 6.93
> surface dust #42 size 7.1
> surface dust #42 size 5.86
> surface dust #42 size 5.91
> surface dust #42 size 6.71
> show #!41 models
> color zone #42 near #41 distance 5.7
> hide #!41 models
> lighting soft
> lighting simple
> graphics silhouettes true
> color zone #42 near #41 distance 5.8
> color zone #42 near #41 distance 5.9
> show #!41 models
> color zone #42 near #41 distance 5.9
> color zone #42 near #41 distance 6.2
> color zone #42 near #41 distance 7.58
> color zone #42 near #41 distance 6.79
> color zone #42 near #41 distance 10.77
> color zone #42 near #41 distance 11.05
> color zone #42 near #41 distance 8.88
> color zone #42 near #41 distance 10.95
> color zone #42 near #41 distance 9.58
> hide #!42 models
> show #!42 models
> color zone #42 near #41 distance 9.68
> color zone #42 near #41 distance 9.6
> color zone #42 near #41 distance 9
> color zone #42 near #41 distance 9.9
> color zone #42 near #41 distance 9.99
> color zone #42 near #41 distance 10.42
> color zone #42 near #41 distance 11.42
> hide #!42 models
> show #!42 models
> lighting soft
> hide #!41 models
> hide #!42 models
> show #!42 models
> lighting simple
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
[Repeated 1 time(s)]
\u2014\u2014\u2014 End of log from Wed Sep 4 05:32:36 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> lighting full
> lighting soft
> lighting simple
> show #2 models
> hide #2 models
> show #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!22 models
> hide #!22 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!3 models
> show #!3 models
> combine #1
> hide #!1 models
> show #!22 models
> hide #!22 models
> rename #22 8xgc_with_polE
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> select #43/L,M,P,Q,N,R,O,S
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> hide (#!43 & sel) target a
> cartoon hide (#!43 & sel)
> hide #2 models
> show #2 models
> hide #2 models
> cartoon (#!43 & sel)
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> hide #!43 models
> show #!43 models
> select #43/2,I
12246 atoms, 12460 bonds, 7 pseudobonds, 1525 residues, 3 models selected
> select ~sel & ##selected
49582 atoms, 50669 bonds, 146 pseudobonds, 6085 residues, 4 models selected
> select #43/2,I,X,Y
14083 atoms, 14513 bonds, 93 pseudobonds, 1615 residues, 4 models selected
> select ~sel & ##selected
47745 atoms, 48616 bonds, 60 pseudobonds, 5995 residues, 3 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> hide #!43 models
> show #!43 models
> rename #43 Tof1_Mcm2_DNA_8xgc
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!43 models
> show #!43 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> ui tool show "Fit in Map"
> hide #!3 models
> show #!3 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> fitmap #3 inMap #8
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 193604 points
correlation = 0.9192, correlation about mean = 0.0445, overlap = 1.418e+04
steps = 72, shift = 2.72, angle = 2.42 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.59052855 0.53373057 -0.60531621 170.37442141
-0.50876033 -0.33602858 -0.79262080 554.64399601
-0.62644949 0.77602608 0.07310647 351.56427577
Axis 0.83279921 0.01121972 -0.55346146
Axis point 0.00000000 138.28597245 467.32476580
Rotation angle (degrees) 109.64532984
Shift along axis -46.46664408
> hide #!8 models
> show #!232 models
> hide #!232 models
> show #!234 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> hide #!234 models
> show #!234 models
> hide #!3 models
> show #!3 models
> fitmap #234 inMap #3
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) using 6114 atoms
average map value = 0.2545, steps = 96
shifted from previous position = 4.78
rotated from previous position = 8.84 degrees
atoms outside contour = 2956, contour level = 0.25
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.05320350 -0.99827136 0.02497348 191.32301696
-0.66299192 0.05401395 0.74667544 251.48569117
-0.74673362 0.02316853 -0.66471958 182.33677195
Axis -0.65199157 0.69542739 0.30213861
Axis point 246.33178982 0.00000000 -20.06616176
Rotation angle (degrees) 146.30004573
Shift along axis 105.24002362
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> hide #!234 models
> show #!177 models
> hide #!177 models
> show #!232 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #43/x
1041 atoms, 1159 bonds, 51 residues, 1 model selected
> color sel black
> select #43/y
796 atoms, 894 bonds, 39 residues, 1 model selected
> color sel gray
> select clear
> select #232/J
3004 atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
> color (#!232 & sel) black
> select #232/I
3006 atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
> color (#!232 & sel) gray
> select clear
> select #232/A#232/E#234/A#234/E
3230 atoms, 3252 bonds, 410 residues, 2 models selected
> ui tool show "Color Actions"
> color sel khaki
[Repeated 4 time(s)]
> color sel peach puff
> color sel moccasin
[Repeated 1 time(s)]
> color sel khaki
[Repeated 4 time(s)]
> select #232/B#232/F#234/B#234/F
2640 atoms, 2652 bonds, 346 residues, 2 models selected
> color sel khaki
[Repeated 1 time(s)]
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> color sel plum
[Repeated 2 time(s)]
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> color sel plum
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume copy #3
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at step 1, values float32
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!43 models
> hide #!42 models
> hide #!44 models
> show #!44 models
> hide #!232 models
> show #!232 models
> ui tool show "Color Zone"
> hide #!44 models
> show #!44 models
> color zone #44 near #232 distance 5.7
> hide #!232 models
> lighting soft
> show #!42 models
> lighting soft
> lighting full
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!43 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color sel hot pink
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #43/I
Alignment identifier is 43/I
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> cartoon hide (#!43 & sel)
> lighting simple
> lighting soft
> show #!8 models
> color #8 #d6d6d6ff models
> color #8 #ebebebff models
> color #8 #ebebeb80 models
> color #8 silver models
[Repeated 1 time(s)]
> color #8 #c0c0c080 models
> color #8 #c0c0c08b models
> color #8 #c0c0c09e models
> color #8 #c0c0c0f5 models
> color #8 #c0c0c0f1 models
> color #8 #c0c0c0ad models
> color #8 #c0c0c0a1 models
> color #8 #c0c0c0ab models
> color #8 #c0c0c0ad models
> color #8 #c0c0c0b4 models
> color #8 #c0c0c0b6 models
> color #8 #c0c0c0b9 models
> color #8 #c0c0c0bd models
> color #8 #c0c0c0c1 models
> color #8 #c0c0c0bf models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #43/I:641
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:641-642
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:649
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #43/I:649-650
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #43/I:630
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:630-631
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:621
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:621-622
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I
6057 atoms, 6171 bonds, 2 pseudobonds, 745 residues, 2 models selected
> color sel slate blue
[Repeated 1 time(s)]
> color sel medium slate blue
> color sel slate blue
[Repeated 6 time(s)]
> color sel medium slate blue
> color sel medium orchid
> color sel dark orchid
> color sel magenta
> color sel dark slate blue
> color sel slate blue
> color sel violet
> color sel slate blue
> color sel medium slate blue
[Repeated 1 time(s)]
> select clear
> select #43/I:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> color sel light coral
> show #!8 models
> hide #!8 models
> select clear
> select #43/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616,618-619
31 atoms, 29 bonds, 3 residues, 1 model selected
> select #43/I:616,618-619,621-622
49 atoms, 46 bonds, 5 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 49 atom styles
> color sel dodger blue
> color sel royal blue
> color sel deep sky blue
> style sel ball
Changed 49 atom styles
> style sel sphere
Changed 49 atom styles
> style sel stick
Changed 49 atom styles
> style sel ball
Changed 49 atom styles
> select clear
> select #43/I:616,618-619,621-622,629
57 atoms, 53 bonds, 6 residues, 1 model selected
> select #43/I:616,618-619,621-622,629
57 atoms, 53 bonds, 6 residues, 1 model selected
> select
> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
4271 atoms, 4319 bonds, 523 residues, 1 model selected
> select clear
> select
> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
4271 atoms, 4319 bonds, 523 residues, 1 model selected
> select clear
> select #43/I:629
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:629
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:629,635-637
35 atoms, 33 bonds, 4 residues, 1 model selected
> select #43/I:629,635-637,640
43 atoms, 40 bonds, 5 residues, 1 model selected
> select #43/I:629,635-637,640,642-643
60 atoms, 56 bonds, 7 residues, 1 model selected
> select #43/I:629,635-637,640,642-643,646
68 atoms, 63 bonds, 8 residues, 1 model selected
> show sel target ab
> color sel crimson
> style sel ball
Changed 68 atom styles
> select clear
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #00fdffff models
> color #8 #73fdffff models
> color #8 #009193ff models
> color #8 #00fdffff models
> color #8 #76d6ffff models
> color #8 #00fdffff models
> color #8 #76d6ffff models
> color #8 #76d6ffd2 models
> color #8 #76d6ff85 models
> color #8 #76d6ff86 models
> color #8 #76d6ffa6 models
> color #8 #76d6ff80 models
> lighting full
> hide #!8 models
> show #!8 models
> hide #!8 models
> lighting soft
> lighting full
> lighting soft
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
> supersample 6 width 2000 transparentBackground true
> lighting full
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
> supersample 6 width 2000 transparentBackground true
> hide #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
> supersample 6 width 2000 transparentBackground true
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
> supersample 6 width 2000 transparentBackground true
> hide #!42 models
> hide #!44 models
> show #!8 models
> color #8 #76d6ffff models
> lighting soft
> lighting full
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
> supersample 6 width 2000 transparentBackground true
> ui tool show "Hide Dust"
> surface dust #8 size 5.7
> surface dust #8 size 5.94
> surface dust #8 size 8.07
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
> supersample 6 width 2000 transparentBackground true
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
> hide #!8 models
> volume #45 step 1
> show #!8 models
> lighting simple
> select add #8
2 models selected
> view sel
> select subtract #8
Nothing selected
> hide #!8 models
> show #!42 models
> show #!44 models
> show #!43 models
> lighting soft
> lighting full
> lighting soft
> lighting full
> hide #!44 models
> hide #!43 models
> hide #!42 models
> show #!45 models
> hide #!45 models
> show #!8 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
> up_single_map.png supersample 6 width 2000 transparentBackground true
> hide #!8 models
> show #!42 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
> up_composite_map.png supersample 6 width 2000 transparentBackground true
> hide #!44 models
> hide #!43 models
> hide #!42 models
> show #!44 models
> show #!232 models
> hide #!232 models
> show #!232 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> select subtract #232
Nothing selected
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view matrix models
> #232,-0.029351,-0.99871,0.041463,192.22,-0.84724,0.046867,0.52914,242.8,-0.5304,-0.019599,-0.84752,167.58
> view matrix models
> #232,-0.020898,-0.996,0.086876,194.54,-0.84044,0.064565,0.53805,243.54,-0.54151,-0.06177,-0.83842,167.34
> view matrix models
> #232,-0.042506,-0.99356,0.10504,195.69,-0.86935,0.088592,0.48619,241.57,-0.49236,-0.070649,-0.86752,165.27
> view matrix models
> #232,-0.053907,-0.99204,0.11378,196.27,-0.88276,0.1006,0.45894,240.51,-0.46673,-0.0757,-0.88115,164.26
> ui mousemode right "translate selected models"
> view matrix models
> #232,-0.053907,-0.99204,0.11378,197.1,-0.88276,0.1006,0.45894,241.87,-0.46673,-0.0757,-0.88115,162.33
> view matrix models
> #232,-0.053907,-0.99204,0.11378,197.14,-0.88276,0.1006,0.45894,241.9,-0.46673,-0.0757,-0.88115,162.25
> select subtract #232
Nothing selected
> hide #!44 models
> show #!44 models
> fitmap #232 inMap #44
Fit molecule 1id3 (#232) to map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) using 12124
atoms
average map value = 0.2847, steps = 68
shifted from previous position = 3.51
rotated from previous position = 4.37 degrees
atoms outside contour = 5383, contour level = 0.25
Position of 1id3 (#232) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
Matrix rotation and translation
-0.03410625 -0.99613821 0.08090390 194.35377785
-0.72343655 0.08045913 0.68568644 250.18361614
-0.68954791 -0.03514264 -0.72338695 177.33095720
Axis -0.66146232 0.70699818 0.25024222
Axis point 246.51764404 0.00000000 -9.19791182
Rotation angle (degrees) 146.98385179
Shift along axis 92.69735224
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!177 models
> hide #!177 models
> show #!232 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Wed Sep 4 08:32:44 2024 \u2014\u2014\u2014
opened ChimeraX session
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1328_map_sharp_zflip.mrc
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.0365, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #46 step 1
> volume #46 level 0.1209
> volume #46 level 0.27
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #46 inMap #44
Fit map cryosparc_P17_J1328_map_sharp_zflip.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy using 183011 points
correlation = 0.9983, correlation about mean = 0.9843, overlap = 3.392e+04
steps = 136, shift = 8.18, angle = 15.4 degrees
Position of cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
Matrix rotation and translation
0.99999993 0.00020825 0.00029549 -0.11547030
-0.00020819 0.99999995 -0.00022028 0.08133560
-0.00029553 0.00022022 0.99999993 0.01845130
Axis 0.52030825 0.69808953 -0.49188447
Axis point 41.74969574 0.00000000 368.99527237
Rotation angle (degrees) 0.02425404
Shift along axis -0.01237652
> ui tool show "Hide Dust"
> surface dust #46 size 5.7
> surface dust #46 size 5.88
> surface dust #46 size 7.58
> surface undust #46
> surface dust #46 size 7.58
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!42 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1293_003_volume_map.mrc
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.131, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #47 step 1
> volume #47 level 0.2274
> select add #47
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #47,1,0,0,34.934,0,1,0,115.11,0,0,1,-196.72
> ui mousemode right "rotate selected models"
> view matrix models
> #47,0.80862,0.53112,-0.25306,75.22,-0.548,0.52343,-0.65247,630.75,-0.21408,0.66628,0.71431,-166.12
> view matrix models
> #47,-0.052033,0.59696,-0.80058,521.42,-0.88318,-0.4017,-0.24213,761.94,-0.46614,0.69446,0.54813,-35.04
> view matrix models
> #47,-0.56463,0.51635,-0.64387,621.88,-0.70577,-0.70651,0.052329,660.64,-0.42788,0.48397,0.76334,-85.832
> view matrix models
> #47,-0.64839,0.75691,-0.081716,371.53,-0.75724,-0.63011,0.17189,611.51,0.078617,0.17333,0.98172,-248.96
> view matrix models
> #47,-0.77683,0.61612,-0.13012,457.28,-0.62893,-0.76938,0.11179,628.86,-0.031234,0.16868,0.98518,-218.23
> view matrix models
> #47,0.12044,0.50172,0.8566,-162.62,-0.47586,-0.72811,0.49337,425.68,0.87123,-0.46705,0.15105,-7.2804
> view matrix models
> #47,0.92809,0.13752,0.34603,-111.13,-0.079004,-0.83541,0.54392,316.34,0.36388,-0.53214,-0.76447,512.58
> view matrix models
> #47,0.95173,-0.049595,-0.3029,179.09,0.060764,-0.93688,0.34433,377.51,-0.30086,-0.34611,-0.88865,710
> view matrix models
> #47,0.74227,-0.056059,-0.66775,384.14,0.082804,-0.98118,0.17442,448.01,-0.66497,-0.18476,-0.72366,713.19
> view matrix models
> #47,0.70283,0.024432,-0.71094,395.12,0.12328,-0.98847,0.0879,472.34,-0.7006,-0.14942,-0.69774,705.44
> view matrix models
> #47,0.054631,-0.15566,-0.9863,726.27,-0.030531,-0.98757,0.15417,489.48,-0.99804,0.02169,-0.058704,500.1
> view matrix models
> #47,0.60463,-0.27385,-0.74795,501.6,0.099908,-0.90554,0.41232,332.8,-0.79021,-0.32403,-0.52016,698.05
> view matrix models
> #47,0.52044,-0.22451,-0.82386,544.88,0.38474,-0.79968,0.46097,210.17,-0.76231,-0.55688,-0.32981,664.82
> ui mousemode right "translate selected models"
> color #47.1 light gray
> view matrix models
> #47,0.52044,-0.22451,-0.82386,558.57,0.38474,-0.79968,0.46097,110.43,-0.76231,-0.55688,-0.32981,702.7
> view matrix models
> #47,0.52044,-0.22451,-0.82386,437.12,0.38474,-0.79968,0.46097,87.569,-0.76231,-0.55688,-0.32981,677.12
> ui mousemode right "rotate selected models"
> view matrix models
> #47,0.56523,-0.45015,-0.69129,420.43,0.27696,-0.6858,0.67303,9.7394,-0.77705,-0.57187,-0.26296,658.06
> ui mousemode right "translate selected models"
> view matrix models
> #47,0.56523,-0.45015,-0.69129,423.1,0.27696,-0.6858,0.67303,13.1,-0.77705,-0.57187,-0.26296,647.01
> hide #!8 models
> show #!8 models
> fitmap #47 inMap #8
Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
correlation = 0.9671, correlation about mean = 0.6025, overlap = 1.762e+04
steps = 160, shift = 4.19, angle = 15.7 degrees
Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99987281 0.00432290 0.01535233 -6.92417661
-0.00420416 0.99996106 -0.00775858 5.37169883
-0.01538527 0.00769307 0.99985205 1.46498711
Axis 0.43594765 0.86722038 -0.24057941
Axis point 110.65380262 0.00000000 488.49257940
Rotation angle (degrees) 1.01544392
Shift along axis 1.28742242
> select subtract #47
Nothing selected
> hide #!46 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> color #16 #009193ff models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!8 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> fitmap #47 inMap #8
Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
correlation = 0.9671, correlation about mean = 0.6024, overlap = 1.762e+04
steps = 48, shift = 0.0108, angle = 0.0117 degrees
Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99987335 0.00426622 0.01533290 -6.90697298
-0.00414464 0.99995979 -0.00795249 5.42282003
-0.01536621 0.00788795 0.99985082 1.41490067
Axis 0.44553022 0.86344648 -0.23656498
Axis point 106.89545515 -0.00000000 488.26292061
Rotation angle (degrees) 1.01860486
Shift along axis 1.27033373
> hide #!8 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!42 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!46 models
> show #!46 models
> fitmap #44 inMap #46
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
steps = 40, shift = 0.00361, angle = 0.00695 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
0.99999996 -0.00014217 -0.00023873 0.08639737
0.00014220 0.99999998 0.00013580 -0.05048921
0.00023872 -0.00013583 0.99999996 -0.02306461
Axis -0.43914796 -0.77188188 0.45972540
Axis point 78.23841730 0.00000000 344.27567005
Rotation angle (degrees) 0.01772022
Shift along axis -0.00957291
> fitmap #44 inMap #46
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
steps = 40, shift = 0.000257, angle = 0.000437 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
0.99999996 -0.00014232 -0.00024540 0.08755876
0.00014235 0.99999998 0.00013952 -0.05131539
0.00024538 -0.00013955 0.99999996 -0.02371294
Axis -0.44137314 -0.77620112 0.45022392
Axis point 79.27979005 0.00000000 339.72277629
Rotation angle (degrees) 0.01811329
Shift along axis -0.00949115
> hide #!44 models
> show #!44 models
> hide #!46 models
> show #!46 models
> hide #!44 models
> show #!232 models
> show #!234 models
> hide #!232 models
> fitmap #234 inMap #46
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) using 6114 atoms
average map value = 0.2627, steps = 48
shifted from previous position = 0.184
rotated from previous position = 0.919 degrees
atoms outside contour = 3238, contour level = 0.27
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
-0.04201562 -0.99848675 0.03548092 191.85732882
-0.66725181 0.05447399 0.74283754 251.20982793
-0.74364623 0.00753607 -0.66853085 181.90203052
Axis -0.65572927 0.69481226 0.29538966
Axis point 247.93591832 0.00000000 -19.62380013
Rotation angle (degrees) 145.89753760
Shift along axis 102.46918037
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> matchmaker #232/A to #234/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 1id3, chain A (#234) with 1id3, chain A (#232), sequence
alignment score = 617.3
RMSD between 97 pruned atom pairs is 0.000 angstroms; (across all 97 pairs:
0.000)
> hide #!234 models
> show #!234 models
> hide #!46 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!234 models
> ui mousemode right zoom
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel light goldenrod yellow
> color sel light yellow
[Repeated 15 time(s)]
> color sel light goldenrod yellow
[Repeated 1 time(s)]
> color sel yellow
[Repeated 10 time(s)]
> color sel yellow green
[Repeated 16 time(s)]
> color sel lime
> color sel yellow green
[Repeated 7 time(s)]
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> color sel red
> color sel dark red
> color sel crimson
> color sel orange red
> color sel red
[Repeated 1 time(s)]
> color sel crimson
[Repeated 1 time(s)]
> color sel fire brick
[Repeated 4 time(s)]
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> color sel gold
[Repeated 3 time(s)]
> color sel dark orange
> color sel gold
[Repeated 4 time(s)]
> select #232/A#232/E#234/A#234/E
3230 atoms, 3252 bonds, 410 residues, 2 models selected
> color sel dodger blue
> color sel dark blue
> color sel medium blue
> color sel blue
[Repeated 1 time(s)]
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel cyan
> color sel deep sky blue
> color sel light sky blue
[Repeated 2 time(s)]
> color sel sky blue
[Repeated 1 time(s)]
> color sel light steel blue
[Repeated 4 time(s)]
> color sel powder blue
> color sel light steel blue
[Repeated 11 time(s)]
> color sel slate gray
> color sel light slate gray
> color sel cadet blue
> color sel steel blue
[Repeated 5 time(s)]
> color sel blue
[Repeated 3 time(s)]
> color sel medium blue
> color sel blue
[Repeated 3 time(s)]
> color sel dodger blue
> color sel steel blue
[Repeated 4 time(s)]
> select #232/B#232/F#234/B#234/F
2640 atoms, 2652 bonds, 346 residues, 2 models selected
> color sel medium aquamarine
> color sel dark cyan
> color sel medium aquamarine
[Repeated 1 time(s)]
> color sel dark cyan
> color sel turquoise
> color sel medium sea green
[Repeated 2 time(s)]
> color sel sea green
[Repeated 1 time(s)]
> color sel medium sea green
[Repeated 1 time(s)]
> color sel forest green
> color sel medium sea green
[Repeated 1 time(s)]
> color sel forest green
> color sel medium sea green
[Repeated 3 time(s)]
> select clear
> show #!235 models
> hide #!235 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> color #47 #d3d3d381 models
> color #47 #d6d6d6ff models
> color #47 silver models
> color #47 #c0c0c082 models
> color #47 #c0c0c0c8 models
> color #47 #c0c0c0c5 models
> color #47 #c0c0c0c1 models
> color #47 #c0c0c0be models
> color #47 #c0c0c0c2 models
> color #47 #c0c0c0c1 models
> color #47 #c0c0c0be models
> color #47 #c0c0c0c0 models
> color #47 #c0c0c0bf models
> hide #!232 models
> show #!232 models
> hide #!47 models
> hide #!42 models
> show #!42 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> hide #!47 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!232 models
> show #!232 models
> hide #!42 models
> show #!42 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!41 models
> hide #!41 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!1 models
> show #!1 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!22 models
> hide #!22 models
> show #!177 models
> hide #!177 models
> show #!177 models
> show #!232 models
> hide #!232 models
> hide #!177 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> show #!38 models
> hide #!1 models
> show #!1 models
> hide #!38 models
> show #!40 models
> hide #!40 models
> combine #1
> hide #!48 models
> show #!48 models
> hide #!1 models
> hide #!48 models
> show #!48 models
> select #48/X,Y
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> select ~sel & ##selected
69387 atoms, 70556 bonds, 77 pseudobonds, 8899 residues, 3 models selected
> delete atoms (#!48 & sel)
> delete bonds (#!48 & sel)
> hide #!48 models
> show #!48 models
> rename #48 DNA_8xgc
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> select #48/X
1041 atoms, 1159 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel black
> select #48/Y
796 atoms, 894 bonds, 39 residues, 1 model selected
> color sel gray
> color sel dark gray
> color sel dim gray
> select clear
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!40 models
> show #!40 models
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!40 models
> show #!40 models
> hide #!48 models
> hide #!40 models
> show #!8 models
> hide #!8 models
> show #!19 models
> hide #!19 models
> show #!42 models
> show #!48 models
> fitmap #48 inMap #42
Fit molecule DNA_8xgc (#48) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
copy (#42) using 1837 atoms
average map value = 0.2869, steps = 136
shifted from previous position = 2.41
rotated from previous position = 2.94 degrees
atoms outside contour = 1074, contour level = 0.3
Position of DNA_8xgc (#48) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
Matrix rotation and translation
0.97626723 0.21196039 0.04444217 20.25889577
0.20777495 -0.97457455 0.08386920 422.39463428
0.06108915 -0.07264478 -0.99548524 498.45034022
Axis -0.99403982 -0.10572708 -0.02658227
Axis point 0.00000000 219.96323566 240.74169709
Rotation angle (degrees) 175.48464775
Shift along axis -78.04663897
> hide #!48 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!234 models
> hide #!234 models
> show #!232 models
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
[Repeated 3 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> show #!234 models
> hide #!232 models
> hide #!42 models
> show #!41 models
> select #41/G
6693 atoms, 6778 bonds, 2 pseudobonds, 422 residues, 2 models selected
> select #41/H,G,F
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> select
> #1/F#1/G#1/H#22/F#22/G#22/H#37/F#37/G#37/H#41/F#41/G#41/H#177/F#177/G#177/H
81053 atoms, 82328 bonds, 30 pseudobonds, 6355 residues, 10 models selected
> color sel royal blue
[Repeated 2 time(s)]
> color sel slate gray
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> color sel light sky blue
> color sel light blue
> color sel powder blue
> color sel deep sky blue
[Repeated 2 time(s)]
> color sel cyan
> color sel deep sky blue
[Repeated 2 time(s)]
> color sel dark turquoise
> color sel deep sky blue
> color sel steel blue
> color sel royal blue
> color sel dodger blue
> color sel deep sky blue
[Repeated 8 time(s)]
> select #1/I#22/I#38/X#41/X#43/I#177/X
51141 atoms, 51789 bonds, 27 pseudobonds, 4230 residues, 12 models selected
> color sel medium slate blue
[Repeated 1 time(s)]
> color sel slate blue
> color sel medium slate blue
> color sel medium orchid
> color sel dark slate blue
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
> color sel indigo
> color sel medium purple
[Repeated 4 time(s)]
> color sel medium slate blue
> color sel medium purple
> color sel medium slate blue
[Repeated 1 time(s)]
> color sel slate blue
> color sel medium slate blue
[Repeated 5 time(s)]
> select clear
> combine #1
> hide #!49 models
> show #!49 models
> select #49/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select ~sel & ##selected
65035 atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
> delete atoms (#!49 & sel)
> delete bonds (#!49 & sel)
> rename #49 N-term-Mcm2_8xgc
> select add #49
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color sel hot pink
> select clear
> matchmaker #49/2 to #23/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker N-Mcm2_6skl, chain 2 (#23) with N-term-Mcm2_8xgc, chain 2 (#49),
sequence alignment score = 3482.9
RMSD between 276 pruned atom pairs is 0.698 angstroms; (across all 293 pairs:
0.967)
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #49/2
Alignment identifier is 49/2
> select #49/2:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #49/2:126-152
214 atoms, 215 bonds, 27 residues, 1 model selected
> select ~sel & ##selected
5975 atoms, 6074 bonds, 5 pseudobonds, 753 residues, 3 models selected
> delete atoms (#!49 & sel)
> delete bonds (#!49 & sel)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 16:21:36 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!48 models
> hide #!48 models
> hide #!49 models
> show #!49 models
> rename #49 N-patch-Mcm2_8xgc
> show #!43 models
> hide #!43 models
> show #!43 models
> ui tool show Matchmaker
> matchmaker #43/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
sequence alignment score = 5320.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #43/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
sequence alignment score = 5320.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!49 models
> hide #!43 models
> hide #!41 models
> show #!178 models
> hide #!178 models
> open /Users/cvetkom/Documents/cryoSPARC/J842_005_volume_map_EMReady.mrc
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 0.116, step 4, values float32
> volume #50 level 3.037
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #50 step 1
> volume #50 level 2.102
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!9 models
> hide #!9 models
> show #!47 models
> hide #!50 models
> show #!50 models
> show #!42 models
> select add #50
2 models selected
> lighting simple
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #50,1,0,0,-65.632,0,1,0,-229.59,0,0,1,71.364
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.4343,-0.44532,0.78299,-22.581,0.48395,0.84849,0.21414,-387.73,-0.75972,0.28593,0.58401,330.58
> ui mousemode right "move picked models"
> view matrix models
> #50,0.4343,-0.44532,0.78299,26.602,0.48395,0.84849,0.21414,-312.09,-0.75972,0.28593,0.58401,140.59
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-144.45,0.53432,0.73727,-0.41346,-106.79,-0.57506,0.67555,0.46146,19.955
> ui mousemode right "translate selected models"
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-121.97,0.53432,0.73727,-0.41346,-120.25,-0.57506,0.67555,0.46146,29.342
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-138.14,0.53432,0.73727,-0.41346,-168.26,-0.57506,0.67555,0.46146,-2.6429
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.59893,-0.097848,0.7948,-111.13,0.56367,0.7565,-0.33163,-206.33,-0.56881,0.64663,0.50825,-10.607
> ui mousemode right zoom
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> select add #47
4 models selected
> select subtract #47
2 models selected
> hide #!47 models
> show #!47 models
> select subtract #50
Nothing selected
> select add #50
2 models selected
> select subtract #50
Nothing selected
> hide #!50 models
> show #!50 models
> hide #!42 models
> show #!42 models
> fitmap #50 inMap #42
Fit map J842_005_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map_sharp.mrc copy using 773474 points
correlation = 0.9586, correlation about mean = 0.8187, overlap = 1.895e+06
steps = 176, shift = 18.3, angle = 13 degrees
Position of J842_005_volume_map_EMReady.mrc (#50) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 0.00008926 0.00001426 -0.02716721
-0.00008926 1.00000000 0.00004509 0.03060850
-0.00001425 -0.00004509 1.00000000 0.00885891
Axis -0.44634943 0.14111659 -0.88366187
Axis point 329.25912566 261.27343201 0.00000000
Rotation angle (degrees) 0.00578781
Shift along axis 0.00861716
> hide #!42 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> volume #47 level 0.3135
> volume #47 level 0.3842
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> volume #47 level 0.3043
> volume #47 level 0.2735
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> ui mousemode right "map eraser"
> hide #!47 models
> show #!47 models
> hide #!50 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_2.cxs
> volume erase #47 center 193.29,217.64,214.85 radius 57.536
Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!52 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!46 models
> show #!42 models
> hide #!42 models
> show #!50 models
> hide #!52 models
> show #!52 models
> close #52
> show #!49 models
> hide #!49 models
> show #!49 models
> hide #!49 models
> show #!47 models
> hide #!46 models
> hide #!50 models
> volume erase #47 center 179.18,226.56,216.65 radius 57.536
Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #51 models
> show #!46 models
> volume add #46,52
Opened volume sum as #53, grid size 1018,965,865, pixel 0.95, shown at step 1,
values float32
> volume #53 level 0.3701
> volume #53 level 0.4202
> volume #53 level 0.4569
> volume #53 level 0.5103
> select add #53
2 models selected
> close #53
> show #51 models
> hide #51 models
> show #!50 models
> show #!48 models
> hide #!48 models
> hide #!234 models
> show #!47 models
> volume add #47,50
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at step 1,
values float32
> volume #53 level 0.3458
> volume #53 level 0.4721
> volume #53 level 0.3819
> volume #53 level 0.2374
> volume #53 level 0.2555
[Repeated 1 time(s)]
> show #!47 models
> hide #!47 models
> show #!46 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> show #!232 models
> hide #!234 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> close #45,236
> show #!235 models
> close #235
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!178 models
> hide #!178 models
> close #178-179
> show #!52 models
> hide #!52 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> show #!46 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> close #44
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> close #16-21
> show #!15 models
> hide #!15 models
> show #!15 models
> close #15
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> close #12
> show #!14 models
> hide #!14 models
> hide #!46 models
> hide #!53 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> color #13 #b2ffff7e models
> color #13 #b2ffffb3 models
> color #13 #b2ffffc2 models
> close #23-40
> show #!22 models
> close #22
> show #!1 models
> hide #!1 models
> show #2 models
> select add #2
24908 atoms, 25142 bonds, 1555 residues, 1 model selected
> close #2
> show #!11 models
> hide #!11 models
> close #11
> show #!10 models
> close #10
> show #!9 models
> hide #!9 models
> close #9
> show #!8 models
> show #!7 models
> hide #!8 models
> close #7
> show #!6 models
> close #6
> show #!5 models
> close #5
> show #!4 models
> close #4
> show #!8 models
> hide #!8 models
> show #!3 models
> close #3
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> rename #234 histones
> show #!233 models
> hide #!234 models
> show #!46 models
> hide #!233 models
> show #!233 models
> hide #!13 models
> hide #!233 models
> show #!233 models
> hide #!46 models
> show #!46 models
> hide #!233 models
> show #!233 models
> hide #!46 models
> color #233 #b2b2b27c models
> show #!232 models
> color #233 #b2b2b27d models
> show #!41 models
> hide #!41 models
> show #!14 models
> hide #!233 models
> hide #!14 models
> show #!13 models
> close #14
> show #!8 models
> hide #!13 models
> hide #!8 models
> rename #1 Zhai
> show #!8 models
> rename #8 consensus_extended.mrc
> show #!13 models
> hide #!8 models
> rename #13 "deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z
> flip"
> show #!41 models
> hide #!13 models
> hide #!41 models
> show #!41 models
> rename #41 fitted_replisome
> show #!42 models
> hide #!41 models
> rename #42 "sharpened_replisome.mrc copy"
> show #!43 models
> hide #!42 models
> hide #!232 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!233 models
> hide #!46 models
> show #!13 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!233 models
> hide #!232 models
> show #!232 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!41 models
> hide #!41 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> rename #233 hetero_ref_good_nucleosome.mrc
> hide #!232 models
> show #!232 models
> rename #232 full_nucleosome
> show #!177 models
> hide #!232 models
> hide #!233 models
> rename #177 Baretic
> show #!53 models
> hide #!177 models
> show #!52 models
> hide #!53 models
> hide #!52 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!46 models
> hide #!43 models
> hide #!13 models
> rename #52 bad_nucleosome
> show #!50 models
> volume add #47,50
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at step 1,
values float32
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!53 models
> hide #!52 models
> close #51
> show #!50 models
> hide #!2 models
> show #!49 models
> hide #!50 models
> ui mousemode right zoom
> close #3
> show #!41 models
> combine #41 #49
Remapping chain ID '2' in N-patch-Mcm2_8xgc #49 to 'AD'
> close #41
> close #49
> hide #!3 models
> show #!3 models
> rename #3 full_replisome
> show #!2 models
> hide #!2 models
> show #!2 models
> close #4
> show #!233 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> color #233 #b2b2b2ff models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #!233 models
> show #!2 models
> show #!232 models
> combine #232
> rename #4 trimmed_nucleosome
> hide #!2 models
> select #13
2 models selected
> view sel
> select #232/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #232/I
Alignment identifier is 232/I
> sequence chain #232/J
Alignment identifier is 232/J
> select #232/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #232/I:1-21
422 atoms, 472 bonds, 21 residues, 1 model selected
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> delete atoms sel
> delete bonds sel
> select #232/J:292
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #232/J:255-292
786 atoms, 882 bonds, 38 residues, 1 model selected
> hide #!232 models
> hide #!4 models
> show #!4 models
> rename #4 full_nucleosome
> rename #232 trimmed_nucleosome
> show #!232 models
> hide #!4 models
> combine #232/I,J
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show #232/I,J
> undo
> select ~sel & ##selected
10916 atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
> select ~sel & ##selected
786 atoms, 882 bonds, 38 residues, 1 model selected
> select ~sel & ##selected
10916 atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
> select #232/I,J
5588 atoms, 6235 bonds, 185 pseudobonds, 301 residues, 3 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel ball
Changed 5588 atom styles
> select #232/J:162
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #232/J:162
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #232/J:147-162
318 atoms, 355 bonds, 16 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> close #5
> show #!4 models
> hide #!4 models
> undo
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> undo
[Repeated 5 time(s)]
> close #232
> show #!4 models
> combine #4
> rename #5 trimmedfull_nucleosome
> rename #5 trimmed_nucleosome
> show #!13 models
> select #4/I,J
6010 atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 6010 atom styles
> select clear
> select #4/I:20@O4
1 atom, 1 residue, 1 model selected
> select clear
> select #4/I:20@C7
1 atom, 1 residue, 1 model selected
> select add #4/J:274@O2
2 atoms, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #5/I
Alignment identifier is 5/I
> sequence chain #5/J
Alignment identifier is 5/J
> hide #!4 models
> select #5/I,J
6010 atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 6010 atom styles
> select #5/I:20@C7
1 atom, 1 residue, 1 model selected
> select add #5/J:274@C7
2 atoms, 2 residues, 1 model selected
> select #5/J:274
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/J:274-292
394 atoms, 441 bonds, 19 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:1-21
422 atoms, 472 bonds, 21 residues, 1 model selected
> select #5/I:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:1-20
402 atoms, 450 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 white models
> color #2 #ffffff83 models
> color #2 #ffffff82 models
> show #!48 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #48
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 1837 atom styles
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #48/X:25
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #5/I:93
41 atoms, 44 bonds, 2 residues, 2 models selected
> select add #48/X:14
61 atoms, 65 bonds, 3 residues, 2 models selected
> select add #48/Y:37
81 atoms, 86 bonds, 4 residues, 2 models selected
> select add #48/Y:48
102 atoms, 109 bonds, 5 residues, 2 models selected
> combine #48
> rename #6 Zhai_DNA_trimmed
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/X
Alignment identifier is 6/X
> sequence chain #6/Y
Alignment identifier is 6/Y
> rename #6 Zhai_DNA
> rename #48 Zhai_DNA_trimmed
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #48/X
Alignment identifier is 48/X
> sequence chain #48/Y
Alignment identifier is 48/Y
> select #48/X:14
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/X:14-25
245 atoms, 273 bonds, 12 residues, 1 model selected
> select #48/X:13
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #48/X:9-13
103 atoms, 115 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/X:26
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/X:26-59
693 atoms, 769 bonds, 34 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/Y:32
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #48/Y:15-32
365 atoms, 410 bonds, 18 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/Y:49
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/Y:49-53
102 atoms, 113 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!6 models
> ui tool show "Fit in Map"
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #48 inMap #2
Fit molecule Zhai_DNA_trimmed (#48) to map volume sum (#2) using 574 atoms
average map value = 4.031, steps = 592
shifted from previous position = 14.2
rotated from previous position = 167 degrees
atoms outside contour = 5, contour level = 0.27354
Position of Zhai_DNA_trimmed (#48) relative to volume sum (#2) coordinates:
Matrix rotation and translation
-0.91975243 -0.27575503 0.27931101 510.33728112
-0.23429189 -0.18521113 -0.95436061 602.17741898
0.31490125 -0.94321578 0.10574123 368.51075021
Axis 0.19984288 -0.63818439 0.74349412
Axis point 200.04559281 464.04730525 0.00000000
Rotation angle (degrees) 178.40215888
Shift along axis -8.32738387
> volume #52 level 0.3197
> volume #2 level 0.9596
> volume #2 level 1.05
> hide #!2 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #48/X to #1/6 pairing ss
Match chain (Zhai_DNA_trimmed (#48) chain X) not compatible with BLOSUM-62
similarity matrix
> close #48
> show #!6 models
> combine #6
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
118294 atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
> select add #5
129622 atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #2 near #3 distance 2.68
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #5
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> color zone #2 near sel distance 2.68
[Repeated 1 time(s)]
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!52 models
> hide #!13 models
> select subtract #5
2 models selected
> select add #5
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #3
129622 atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
> color zone #2 near sel distance 2.68
> hide #!5 models
> hide #!3 models
> volume #233 level 2.785
> volume #2 level 1.357
> volume #2 level 0.8512
> volume #2 level 0.4721
> volume #2 level 0.3096
> color zone #2 near sel distance 5
> color zone #2 near sel distance 3
> color zone #2 near sel distance 3.5
> color zone #2 near sel distance 4
[Repeated 1 time(s)]
> volume splitbyzone #2
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 1 as #9.2, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 2 as #9.3, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 3 as #9.4, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 4 as #9.5, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 5 as #9.6, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 6 as #9.7, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 7 as #9.8, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 8 as #9.9, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 9 as #9.10, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 10 as #9.11, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 11 as #9.12, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 12 as #9.13, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 13 as #9.14, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 14 as #9.15, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 15 as #9.16, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 16 as #9.17, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 17 as #9.18, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
> close #9.2-18
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!9.1 models
> hide #!9 models
> select #6/X:25
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #6/Y:37@C3'
22 atoms, 23 bonds, 2 residues, 1 model selected
> select add #6/Y:38
41 atoms, 43 bonds, 3 residues, 1 model selected
> select subtract #6/Y:37
40 atoms, 43 bonds, 2 residues, 1 model selected
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/X
Alignment identifier is 6/X
> sequence chain #6/Y
Alignment identifier is 6/Y
> select #6/X:26
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/X:26-59
693 atoms, 769 bonds, 34 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/Y:34
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #6/Y:34-53
411 atoms, 461 bonds, 20 residues, 1 model selected
> select #6/Y:36
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:36-53
370 atoms, 415 bonds, 18 residues, 1 model selected
> select #6/Y:39
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/Y:39-53
310 atoms, 348 bonds, 15 residues, 1 model selected
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!7 models
> select #6/Y:38
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #6/Y:15-38
486 atoms, 545 bonds, 24 residues, 1 model selected
> hide #!3 models
> select #6/Y:36
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:15-36
447 atoms, 502 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!9.1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #6/X:15
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #6/X:14
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/X:13
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/X:9-13
103 atoms, 115 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/Y:53
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:49-53
102 atoms, 113 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show "Fit in Map"
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> fitmap #6 inMap #9.1
Fit molecule Zhai_DNA (#6) to map volume sum 0 (#9.1) using 492 atoms
average map value = 2.428, steps = 112
shifted from previous position = 2.38
rotated from previous position = 20.2 degrees
atoms outside contour = 57, contour level = 0.30965
Position of Zhai_DNA (#6) relative to volume sum 0 (#9.1) coordinates:
Matrix rotation and translation
0.84252921 0.47835125 0.24763810 -39.97421560
-0.52899667 0.64815172 0.54777905 144.67789487
0.10152374 -0.59251958 0.79913296 198.24507755
Axis -0.74601377 0.09559191 -0.65903387
Axis point 0.00000000 273.04359310 -103.91847500
Rotation angle (degrees) 49.84130149
Shift along axis -86.99886895
> show #!3 models
> show #!5 models
> select #5/I
2604 atoms, 2903 bonds, 3 pseudobonds, 142 residues, 2 models selected
> color (#!5 & sel) black
> select #5/J
2610 atoms, 2912 bonds, 5 pseudobonds, 141 residues, 2 models selected
> color (#!5 & sel) dim gray
> select clear
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select add #3
118294 atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!9.1 models
> hide #!9 models
> show #!2 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> combine #3 #6 #5
Remapping chain ID 'X' in Zhai_DNA #6 to 'Z'
Remapping chain ID 'Y' in Zhai_DNA #6 to 'a'
Remapping chain ID 'A' in trimmed_nucleosome #5 to 'K'
Remapping chain ID 'B' in trimmed_nucleosome #5 to 'L'
Remapping chain ID 'C' in trimmed_nucleosome #5 to 'M'
Remapping chain ID 'D' in trimmed_nucleosome #5 to 'N'
Remapping chain ID 'E' in trimmed_nucleosome #5 to 'O'
Remapping chain ID 'F' in trimmed_nucleosome #5 to 'P'
Remapping chain ID 'G' in trimmed_nucleosome #5 to 'Q'
Remapping chain ID 'H' in trimmed_nucleosome #5 to 'R'
Remapping chain ID 'I' in trimmed_nucleosome #5 to 'S'
Remapping chain ID 'J' in trimmed_nucleosome #5 to 'T'
> hide #!10 models
> show #!10 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!2 models
> close #6-7
> rename #10 extended_structure
> hide #!10 models
> show #!10 models
> select add #10
130114 atoms, 131991 bonds, 312 pseudobonds, 8456 residues, 4 models selected
> color zone #2 near sel distance 4.25
> color zone #2 near sel distance 53.56
[Repeated 1 time(s)]
> select clear
> volume #2 level 0.1833
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!13 models
> hide #!10 models
> hide #!2 models
Drag select of 6 atoms, 7 residues, 5 bonds
Drag select of 1 atoms, 4 residues, 1 bonds
Drag select of 48 atoms, 44 residues, 38 bonds
Drag select of 66 atoms, 50 residues, 55 bonds
> select #43/X,Y
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #43/I:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #43/I:657
13 atoms, 11 bonds, 2 residues, 1 model selected
> hide #!3 models
> select clear
Drag select of 35 atoms, 28 residues, 30 bonds
Drag select of 14 atoms, 18 residues, 11 bonds
Drag select of 8 residues
> select ~sel & ##selected
11865 atoms, 12085 bonds, 7 pseudobonds, 1480 residues, 3 models selected
> cartoon hide (#!43 & sel)
> cartoon (#!43 & sel)
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #43/I
Alignment identifier is 43/I
> select #43/I:605-606
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:11-606
4587 atoms, 4671 bonds, 2 pseudobonds, 570 residues, 2 models selected
> cartoon hide (#!43 & sel)
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> select #43/I:658
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:658-781
1061 atoms, 1089 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #43
6598 atoms, 6698 bonds, 5 pseudobonds, 831 residues, 3 models selected
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
Drag select of 78 atoms, 55 residues, 65 bonds
> color sel red
> combine #43,3
Remapping chain ID 'I' in full_replisome #3 to 'K'
> hide #!6 models
> show #!6 models
> close #3
> rename #6 full_replisome
> combine #5,6
Remapping chain ID 'A' in full_replisome #6 to 'L'
Remapping chain ID 'B' in full_replisome #6 to 'M'
Remapping chain ID 'C' in full_replisome #6 to 'N'
Remapping chain ID 'D' in full_replisome #6 to 'O'
Remapping chain ID 'E' in full_replisome #6 to 'P'
Remapping chain ID 'F' in full_replisome #6 to 'Q'
Remapping chain ID 'G' in full_replisome #6 to 'R'
Remapping chain ID 'H' in full_replisome #6 to 'S'
Remapping chain ID 'I' in full_replisome #6 to 'T'
Remapping chain ID 'J' in full_replisome #6 to 'U'
> close #10
> rename #3 extended_structure
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 19:04:03 2024 \u2014\u2014\u2014
opened ChimeraX session
> open /Users/cvetkom/Desktop/extended_structure_old.pdb
Chain information for extended_structure_old.pdb #7
---
Chain | Description
0 7 | No description available
2 5 AD | No description available
3 6 | No description available
4 9 | No description available
8 AB | No description available
A | No description available
AA AC | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F G H | No description available
I | No description available
J | No description available
K O | No description available
L P | No description available
M Q | No description available
N R | No description available
S T | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> matchmaker #7/2 to #3/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#3) with extended_structure_old.pdb,
chain 2 (#7), sequence alignment score = 3554.3
RMSD between 293 pruned atom pairs is 0.000 angstroms; (across all 293 pairs:
0.000)
> select #7/a,Z
492 atoms, 550 bonds, 24 residues, 1 model selected
> select ~sel & ##selected
129622 atoms, 131441 bonds, 58 pseudobonds, 8432 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/a
247 atoms, 277 bonds, 12 residues, 1 model selected
> color sel dim gray
> select #7/Z
245 atoms, 273 bonds, 12 residues, 1 model selected
> color sel black
> combine #3,7
> hide #!10 models
> show #!10 models
> hide #!3 models
> hide #!7 models
> close #3,7
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!43 models
> hide #!6 models
> hide #!10 models
> show #!10 models
> rename #10 extended_structure
> select #10,T
Expected an objects specifier or a keyword
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
[Repeated 2 time(s)]
> select clear
> show #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> select add #10
130523 atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
> ui tool show "Color Zone"
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 10
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 15
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 20
[Repeated 1 time(s)]
> select clear
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> volume splitbyzone #2
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
> volume #3.4 level 0.2577
> volume #3.4 level 0.1585
> volume #3.5 level 0.2148
> volume #3.4 level 0.183
> volume #3.5 level 0.183
> volume #3.9 level 0.9634
> volume #3.9 level 2.784
> volume #3.10 level 2.78
> volume #3.11 level 2.78
> volume #3.13 level 2.78
> volume #3.14 level 2.78
> volume #3.16 level 2.78
> volume #3.17 level 2.78
> volume #3.18 level 2.78
> volume #3.15 level 2.78
> volume #3.12 level 2.78
> volume copy #3.8
Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> volume #3.8 level 2.78
> volume #7 color #7b68ee7c
> volume #7 color #7b68ee33
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #!7 models
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> color zone #7 near sel distance 5.7
> show #!7 models
> volume #7 color #ff2600
> ui tool show "Color Actions"
> color sel medium slate blue
> select #7
2 models selected
> color sel medium slate blue
> volume #7 color #ff260081
> color sel medium slate blue
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> color sel purple
> color sel magenta
> color zone #7 near sel distance 5.7
> volume splitbyzone #7
Opened volume sum 7 copy 0 as #11.1, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
> close #11.1
> show #!7 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!5 models
> select add #5
11737 atoms, 12370 bonds, 187 pseudobonds, 1146 residues, 4 models selected
> color zone #13 near sel distance 5.7
> color zone #13 near sel distance 6.18
> color zone #13 near sel distance 11.5
> select clear
> ui tool show "Hide Dust"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #3.3 size 5.7
> surface dust #3.3 size 5.66
> surface dust #3.3 size 33
> surface dust #3.3 size 33.37
> surface dust #3.3 size 14.12
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 19:48:00 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!11.2 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> rename #7 Tof1_lower_level
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> rename #11 Tof1_HTH_lower_level
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show "Hide Dust"
> hide #!13 models
> show #!13 models
> hide #!11 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> surface dust #13 size 5.7
[Repeated 1 time(s)]
> surface undust #13
> surface dust #13 size 5.7
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> show #!3.1 models
> hide #!3.1 models
> surface dust #3.2 size 5.7
> surface dust #3.2 size 5.68
> surface dust #3.2 size 13.68
> surface undust #3.2
> surface dust #3.2 size 13.68
> surface dust #3.2 size 14.86
[Repeated 1 time(s)]
> surface dust #3.4 size 5.7
> surface dust #3.3 size 14.12
> surface dust #3.3 size 14.38
> surface dust #3.3 size 6.94
> hide #!3.3 models
> show #!3.3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.8 models
> hide #!3.9 models
> hide #!3.10 models
> hide #!3.11 models
> hide #!3.12 models
> hide #!3.13 models
> hide #!3.14 models
> hide #!3.15 models
> hide #!3.16 models
> hide #!3.17 models
> hide #!3.18 models
> hide #!13 models
> surface dust #3.3 size 13.23
> surface undust #3.3
> surface dust #3.3 size 13.23
> ui tool show "Map Eraser"
> volume erase #3.3 center 191.19,155.01,168.45 radius 10.807
> show #!3.2 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> show #!3.8 models
> show #!3.9 models
> show #!3.10 models
> show #!3.11 models
> show #!3.12 models
> show #!3.13 models
> show #!3.14 models
> show #!3.15 models
> show #!3.16 models
> show #!3.17 models
> show #!3.18 models
> show #!5 models
> hide #!5 models
> show #!13 models
> hide #!13 models
> show #!13 models
> surface dust #3.4 size 5.7
> surface undust #3.4
> surface dust #3.4 size 7.66
> surface dust #3.5 size 5.7
> surface dust #3.5 size 6.18
> surface dust #3.5 size 8.89
> surface dust #3.6 size 5.7
> surface dust #3.6 size 5.97
> surface dust #3.6 size 6.94
> surface dust #3.8 size 7.05
> surface dust #3.8 size 7.54
> surface dust #3.8 size 5.15
> surface dust #3.7 size 5.7
> surface undust #3.9
> surface dust #3.9 size 5.7
> surface undust #3.8
> surface dust #3.8 size 5.15
> surface dust #3.9 size 5.7
> hide #!3.5 models
> show #!3.5 models
> surface undust #3.5
> surface dust #3.5 size 8.89
> lighting soft
> hide #!3 models
> show #!3 models
> select add #3
37 models selected
> view sel
> select subtract #3
Nothing selected
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side.png
> supersample 6 width 2000 transparentBackground true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side_back.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> surface dust #7 size 5.7
> surface dust #7 size 6.07
> surface dust #7 size 11.59
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> surface dust #2 size 5.7
> surface dust #2 size 5.97
> surface dust #2 size 35.17
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!2 models
> show #!2 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!42 models
> hide #!2 models
> show #!2 models
> hide #!42 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near #10 distance 19.41
> color zone #2 near #10 distance 13.26
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 16
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 18
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 20
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!13 models
> hide #!10 models
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Side View"
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 22
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 24
> hide #!2 models
> hide #!13 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!10 models
> hide #!10 models
> show #!13 models
> show #!43 models
> hide #!43 models
> show #!10 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> show #!43 models
> hide #!10 models
> hide #!43 models
> show #!43 models
> hide #!3 models
> show #!3 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel magenta
> hide sel target a
> select subtract #43
Nothing selected
> hide #!43 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level.png
> supersample 6 width 2000 transparentBackground true
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level.png
> supersample 6 width 2000 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> show #!1 models
> hide #!3 models
> hide #!13 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> show #!13 models
> show #!43 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!43 models
> show #!43 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11 models
> show #!11 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> color #7 #7b68ee80 models
> color #7 #7b68ee9e models
> color #7 #7b68eea0 models
> color #7 #7b68ee32 models
> color #7 #7b68ee29 models
> color #7 #7b68eeab models
> color #7 #7b68ee89 models
> color #7 #7b68ee8a models
> hide #!43 models
> show #!43 models
> hide #!43 models
> hide #!7 models
> show #!7 models
> show #!43 models
> lighting simple
> lighting full
> lighting soft
> hide #!43 models
> show #!43 models
> hide #!13 models
> show #!13 models
> hide #!7 models
> hide #!13 models
> hide #!3 models
> show #!3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> volume copy #3.2
Opened volume sum 1 copy as #12, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> rename #12 leading_strand_vol_3p2
> volume copy #3.3
Opened volume sum 2 copy as #14, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> hide #!14 models
> show #!14 models
> rename #14 lagging_strand_vol_3p3
> hide #!14 models
> hide #!12 models
> show #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.2 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> surface dust #12 size 5.7
> surface dust #12 size 5.59
> surface dust #12 size 9.82
> surface dust #12 size 5.68
[Repeated 1 time(s)]
> surface undust #12
> surface dust #12 size 5.68
> surface dust #14 size 5.7
> surface dust #14 size 6.18
> surface dust #14 size 21.74
> surface dust #14 size 22.85
> surface dust #14 size 18.43
> surface dust #14 size 19.68
> surface dust #14 size 14.62
> hide #!12 models
> hide #!14 models
> show #!3.2 models
> show #!3.3 models
> surface undust #3.2
> surface dust #3.2 size 14.86
> hide #!3.3 models
> hide #!3.2 models
> show #!12 models
> show #!14 models
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!14 models
> hide #15 models
> show #15 models
> hide #!43 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #15 models
> show #15 models
> volume erase #12 center 219.68,211.59,243.35 radius 53.859
> show #!3 models
> show #!3.2 models
> show #!3.3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume erase #12 center 202.99,259.45,180.39 radius 53.859
> volume erase #12 center 157.95,181.67,182.6 radius 53.859
> volume erase #12 center 178.35,160.14,212.29 radius 53.859
> volume erase #12 center 206.83,165.32,136.53 radius 18.769
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume erase #14 center 196.99,177.22,211.99 radius 31.01
> volume erase #14 center 212.15,214.12,242.94 radius 40.802
> volume erase #14 center 208.55,248.81,191.88 radius 40.802
> volume erase #14 center 168.65,198.46,168.27 radius 40.802
> volume erase #14 center 172.72,159.07,188.6 radius 40.802
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!12 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3.2 models
> hide #!3.3 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!3 models
> show #!3 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!43 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> show #!1 models
> open 8XGC fromDatabase pdb format mmcif
8xgc title:
Structure of yeast replisome associated with FACT and histone hexamer,
Composite map [more info...]
Chain information for 8xgc #15
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
8 | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
9 | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
M | FACT complex subunit POB3 | POB3_YEAST 1-552
N R | Histone H3 | A0A6A5Q536_YEASX 1-136
O S | Histone H4 | H4_YEAST 1-103
P | Histone H2A.1 | H2A1_YEAST 1-132
Q | Histone H2B.2 | H2B2_YEAST 1-131
X | DNA (51-MER) |
Y | DNA (39-MER) |
Non-standard residues in 8xgc #15
---
ADP \u2014 adenosine-5'-diphosphate
ZN \u2014 zinc ion
> show #!177 models
> hide #!177 models
> ui tool show Matchmaker
> matchmaker #15/I to #1/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Zhai, chain I (#1) with 8xgc, chain I (#15), sequence alignment
score = 5609.4
RMSD between 745 pruned atom pairs is 0.000 angstroms; (across all 745 pairs:
0.000)
> select add #15
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> hide (#!15 & sel) target a
> cartoon (#!15 & sel)
> select subtract #15
Nothing selected
> select add #15
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #15
Nothing selected
> hide #!15 models
> select #1/N#1/R#15/N#15/R
2740 atoms, 2766 bonds, 334 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dodger blue
[Repeated 2 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel dodger blue
[Repeated 1 time(s)]
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel cyan
[Repeated 1 time(s)]
> color sel deep sky blue
> color sel dodger blue
> color sel steel blue
> color sel slate blue
> color sel royal blue
> color sel dodger blue
> select #1/O#1/S#15/O#15/S
2534 atoms, 2560 bonds, 316 residues, 2 models selected
> color sel medium spring green
> color sel medium aquamarine
> color sel sea green
> color sel medium sea green
> color sel light sea green
[Repeated 1 time(s)]
> color sel medium spring green
[Repeated 1 time(s)]
> select #1/P#15/P
1406 atoms, 1422 bonds, 182 residues, 2 models selected
> select #1/P#15/P
1406 atoms, 1422 bonds, 182 residues, 2 models selected
> color sel gold
[Repeated 1 time(s)]
> select #1/Q#15/Q
1412 atoms, 1432 bonds, 182 residues, 2 models selected
> color sel crimson
> select #1/L#15/L
6948 atoms, 7044 bonds, 6 pseudobonds, 986 residues, 4 models selected
> color sel salmon
[Repeated 2 time(s)]
> color sel tomato
> color sel salmon
> select #1/M#15/M
3752 atoms, 3736 bonds, 14 pseudobonds, 758 residues, 4 models selected
> color sel sienna
> color sel saddle brown
> color sel brown
[Repeated 1 time(s)]
> color sel tomato
> color sel fire brick
> color sel orange red
> color sel brown
> color sel sienna
> select clear
> lighting simple
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color (#!1 & sel) hot pink
> hide #!1 models
> select add #1
71224 atoms, 72609 bonds, 163 pseudobonds, 8989 residues, 4 models selected
> select subtract #1
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #43/I
Alignment identifier is 43/I
> show #!1 models
> hide #!1 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> color #3.2 #00000081 models
> color #3.2 #0000009d models
> color #3.2 #00000099 models
> color #3.3 #696969a7 models
> color #3.3 #696969a0 models
> color #3.3 #6969699a models
> color #3.3 #69696999 models
> color #3.4 #4682b49a models
> color #3.4 #4682b499 models
> color #3.5 #3cb37193 models
> color #3.5 #3cb37199 models
> color #3.6 #ffd7009c models
> color #3.6 #ffd7009a models
> color #3.6 #ffd70099 models
> hide #!13 models
> show #!13 models
> color #13 #b2ffffbf models
[Repeated 1 time(s)]
> color #13 #b2ffffc5 models
> color #13 #b2ffffc4 models
> color #13 #b2ffffb0 models
> color #13 #b2ffff9f models
> color #13 #b2ffff9b models
> color #13 #b2ffff98 models
> color #13 #b2ffff99 models
> color zone #13 near #10 distance 5.7
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #3.7 #b222229c models
> color #3.7 #b222229b models
> color #3.7 #b2222297 models
> color #3.7 #b2222298 models
> color #3.7 #b2222299 models
> hide #!3.8 models
> show #!3.8 models
> show #!234 models
> hide #!234 models
> hide #!13 models
> show #!13 models
> color #13 #b2ffffff models
> show #!9 models
> hide #!9 models
> hide #!3.18 models
> show #!3.18 models
> hide #!3.17 models
> show #!3.17 models
> hide #!3.8 models
> show #!3.8 models
> color #3.7 firebrick models
> color #3.6 gold models
> color #3.5 mediumseagreen models
> color #3.4 steelblue models
> hide #!3.3 models
> show #!3.3 models
> color #3.3 dimgrey models
> color #3.2 black models
> hide #!13 models
> show #!13 models
> color zone #13 near #10 distance 5.7
[Repeated 1 time(s)]
> color zone #13 near #10 distance 5.87
> color zone #13 near #10 distance 12.76
> ui tool show "Side View"
> lighting soft
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> hide #!13 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616-617
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #43/I:609
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:609
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:609,616
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #43/I:609,616,618-619
40 atoms, 37 bonds, 4 residues, 1 model selected
> select #43/I:609,616,618-619,621-622
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616,632
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #43/I:616,618-619,632
40 atoms, 37 bonds, 4 residues, 1 model selected
> select #43/I:616,618-619,621-622,632
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:616,618-619,621-622,632
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:616,619
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:616,618-619
31 atoms, 29 bonds, 3 residues, 1 model selected
> select #43/I:616,618-619,621-622
49 atoms, 46 bonds, 5 residues, 1 model selected
> show sel target ab
> color sel byhetero
[Repeated 1 time(s)]
> style sel sphere
Changed 49 atom styles
> hide #!12 models
> show #!12 models
> ui tool show "Color Actions"
> color sel cyan
[Repeated 2 time(s)]
> color sel byhetero
[Repeated 1 time(s)]
> select #43/I:616,618-619,621-622,635-636
67 atoms, 63 bonds, 7 residues, 1 model selected
> select #43/I:635
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:635-637
27 atoms, 26 bonds, 3 residues, 1 model selected
> select #43/I:627,635-637
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #43/I:627,629,635-637
44 atoms, 41 bonds, 5 residues, 1 model selected
> select #43/I:627,629,635-637,640
52 atoms, 48 bonds, 6 residues, 1 model selected
> select #43/I:627,629,635-637,640,642-643
69 atoms, 64 bonds, 8 residues, 1 model selected
> select #43/I:627,629,635-637,640,642-643,646
77 atoms, 71 bonds, 9 residues, 1 model selected
> color sel orange red
> show sel target ab
> color sel byhetero
> style sel ball
Changed 77 atom styles
> style sel sphere
Changed 77 atom styles
> color sel orange
> color sel orange red
> color sel gold
> color sel orange
> color sel byhetero
> select add #43
409 atoms, 409 bonds, 51 residues, 1 model selected
> select subtract #43
Nothing selected
> cartoon style #12,14,43#3.8-18#!3 xsection oval modeHelix default
> cartoon style #12,14,43#3.8-18#!3 xsection rectangle modeHelix default
> cartoon style (#12,14,43#3.8-18#!3 & coil) xsection oval
> cartoon style #12,14,43#3.8-18#!3 xsection barbell modeHelix default
> cartoon style #12,14,43#3.8-18#!3 modeHelix tube sides 20
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches.png
> supersample 6 width 2000 transparentBackground true
> show #!13 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_2.png
> supersample 6 width 2000 transparentBackground true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_3.png
> supersample 6 width 2000 transparentBackground true
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select #43/I:607-609
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> hide sel target a
> color sel magenta
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_lighter.png
> supersample 6 width 2000 transparentBackground true
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level_lighter.png
> supersample 6 width 2000 transparentBackground true
> hide #!2 models
> show #!3 models
> show #!7 models
> color #7 #7b68ee81 models
> color #7 #7b68ee80 models
> color #7 #7b68ee73 models
> color #7 #7b68ee41 models
> color #7 #7b68ee96 models
> color #7 #7b68ee8c models
> color #7 #7b68ee95 models
> color #7 #7b68ee9c models
> color #7 #7b68ee96 models
> color #7 #7b68ee99 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> color #11.2 #ff00ff83 models
> color #11.2 #ff00ff3b models
> color #11.2 #ff00ff4d models
> color #11.2 #ff00ff68 models
> color #11.2 #ff00ff77 models
> color #11.2 #ff00ff87 models
> color #11.2 #ff00ff9e models
> color #11.2 #ff00ff9a models
> hide #!11.2 models
> color #11.2 #ff00ff99 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> select #43/I:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> color sel blue violet
[Repeated 2 time(s)]
> color sel blue
> color sel dark blue
> color sel navy
[Repeated 2 time(s)]
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_transp.png
> supersample 6 width 2000 transparentBackground true
> select #43/I:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:607-656
402 atoms, 402 bonds, 50 residues, 1 model selected
> color sel magenta
> select clear
> color #11.2 #ff00ff3b models
> color #11.2 #ff00ff71 models
> color #11.2 magenta models
> color #11.2 white models
> color #11.2 #ffffff72 models
> color #11.2 #ffffff5f models
> color #11.2 #ffffff79 models
> color #11.2 #ffffff4d models
> color #11.2 #ffffff5e models
> color #11.2 #ff40ffff models
> select clear
[Repeated 1 time(s)]
> hide #!11.2 models
> hide #!11 models
> hide #!43 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_flat.png
> supersample 6 width 2000 transparentBackground true
> lighting soft
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_background.png
> supersample 6 width 2000 transparentBackground true
> show #!43 models
> show #!1 models
> hide #!3 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #3.2 black models
> color #3.3 dimgrey models
> color #3.4 steelblue models
> color #3.5 mediumseagreen models
> color #3.6 #ffd700fd models
> color #3.6 gold models
> color #3.7 firebrick models
> hide #!3 models
> show #!3 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> select #1/L,M
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon hide (#!1 & sel)
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
> supersample 6 width 2000 transparentBackground true
> select add #12
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
> select add #14
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 6 models selected
> select subtract #14
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
> select subtract #12
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon (#!1 & sel)
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_with_FACT.png
> supersample 6 width 2000 transparentBackground true
> show #!12 models
> show #!14 models
> hide #!13 models
> hide #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai.png
> supersample 6 width 2000 transparentBackground true
> select #1/L,M
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon hide (#!1 & sel)
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
> supersample 6 width 2000 transparentBackground true
> hide #!12 models
> hide #!14 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!3.7 models
> show #!3.6 models
> show #!3.5 models
> show #!3.4 models
> show #!3.3 models
> show #!3.2 models
> show #!13 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT_wo_nucl.png
> supersample 6 width 2000 transparentBackground true
> cartoon (#!1 & sel)
> select clear
> hide #!1 models
> show #!43 models
> combine #1
> select #16/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select ~sel & ##selected
65035 atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
> show #!7 models
> hide #!7 models
> show #!11 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!11 models
> hide #!11 models
> show #!11 models
> color #11.2 #ff40ffde models
> color #11.2 #ff40ffce models
> color #11.2 #ff40ffcc models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH_density.png
> supersample 6 width 2000 transparentBackground true
> hide #!11 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Mon Sep 9 04:24:31 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!16 models
> show #!16 models
> hide #!1 models
> hide #!16 models
> show #!16 models
> show #!1 models
> combine #1
> hide #!1 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!3 models
> hide #!13 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!17 models
> show #!17 models
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #17/Q to #10/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain D (#10) with copy of Zhai, chain Q (#17),
sequence alignment score = 586.9
RMSD between 88 pruned atom pairs is 0.795 angstroms; (across all 91 pairs:
1.028)
> hide #!10 models
> select #17/Q,P,O,N,S,R,L,M
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> select ~sel & ##selected
61828 atoms, 63129 bonds, 153 pseudobonds, 7610 residues, 4 models selected
> delete atoms (#!17 & sel)
> delete bonds (#!17 & sel)
> show #!8 models
> hide #!8 models
> show #!10 models
> select add #10
130523 atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
> view sel
> select subtract #10
Nothing selected
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> select clear
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #17/L
Alignment identifier is 17/L
> select clear
> select #17/L:961-996
197 atoms, 197 bonds, 36 residues, 1 model selected
> select #17/L:956
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #17/L:948-956
65 atoms, 67 bonds, 9 residues, 1 model selected
> select #17/L:948-950
22 atoms, 23 bonds, 3 residues, 1 model selected
> select #17/L:948-996
262 atoms, 264 bonds, 1 pseudobond, 45 residues, 2 models selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!1 models
> hide #!1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!17 models
> hide #!43 models
> combine #15
> hide #!18 models
> select add #17
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> select subtract #17
Nothing selected
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!1 models
> hide #!1 models
> combine #1
> select #19/Q,P,O,N,S,R,L,M,2
15585 atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
> select ~sel & ##selected
55639 atoms, 56840 bonds, 148 pseudobonds, 6830 residues, 4 models selected
> hide (#!19 & sel) target a
> hide #!19 models
> show #!19 models
> cartoon hide (#!19 & sel)
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!10 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!19 models
> hide #!16 models
> show #!16 models
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!16 models
> hide #!19 models
> show #!19 models
> cartoon (#!19 & sel)
> delete atoms (#!19 & sel)
> delete bonds (#!19 & sel)
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!17 models
> ui tool show Matchmaker
> matchmaker #19/L to #17/L pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of Zhai, chain L (#17) with copy of Zhai, chain L (#19),
sequence alignment score = 4482.1
RMSD between 493 pruned atom pairs is 0.000 angstroms; (across all 493 pairs:
0.000)
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!10 models
> hide #!19 models
> show #!19 models
> select #19/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> select #19/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select add #19
15585 atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
> select subtract #19
Nothing selected
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Wed Sep 11 12:56:29 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> show #!10 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!50 models
> hide #!50 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_sharp.mrc
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map.mrc
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.108, step 4, values float32
> hide #!10 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> volume #20 step 1
> volume #20 level 0.6282
> volume #20 level 0.5581
> volume #21 step 1
> volume #21 level 0.3191
> show #!50 models
> hide #!20 models
> show #!10 models
> hide #!10 models
> show #!20 models
> select add #20
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.99684,0.061516,0.050168,-28.958,-0.064381,0.99626,0.057647,4.4916,-0.046434,-0.060695,0.99708,30.666
> lighting simple
> view matrix models
> #20,0.73598,-0.4705,-0.48679,329.31,0.6768,0.52918,0.51178,-191.97,0.01681,-0.70611,0.7079,265.3
> view matrix models
> #20,0.12559,-0.15204,-0.98036,539.99,-0.57343,0.79527,-0.1968,269.08,0.80957,0.58689,0.012694,-138.71
> view matrix models
> #20,-0.16726,-0.54653,-0.82057,691.05,-0.96595,-0.075783,0.24736,507.43,-0.19738,0.83401,-0.51525,212.61
> view matrix models
> #20,-0.44936,-0.35876,-0.81815,718.23,-0.88005,0.3352,0.33637,346.68,0.15357,0.87116,-0.46636,90.611
> view matrix models
> #20,-0.44063,-0.37463,-0.81578,719.55,-0.88716,0.32048,0.33201,353.87,0.13706,0.87003,-0.47357,97.439
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.44063,-0.37463,-0.81578,705.11,-0.88716,0.32048,0.33201,144.71,0.13706,0.87003,-0.47357,26.598
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.33684,-0.44475,-0.8299,698.78,-0.91245,0.37165,0.17118,178.84,0.2323,0.81491,-0.531,29.613
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.33684,-0.44475,-0.8299,696.83,-0.91245,0.37165,0.17118,160.27,0.2323,0.81491,-0.531,22.667
> ui tool show "Fit in Map"
> fitmap #20 inMap #50
Fit map cryosparc_P17_J819_005_volume_map_sharp.mrc in map
J842_005_volume_map_EMReady.mrc using 218333 points
correlation = 0.9383, correlation about mean = 0.6201, overlap = 1.633e+06
steps = 320, shift = 3.21, angle = 32.8 degrees
Position of cryosparc_P17_J819_005_volume_map_sharp.mrc (#20) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
-0.97651784 -0.21085655 -0.04418632 623.63633661
-0.20170911 0.96689998 -0.15626218 100.15142454
0.07567265 -0.14368002 -0.98672676 575.82401984
Axis 0.10410159 -0.99168284 0.07568362
Axis point 308.30489723 0.00000000 301.22875456
Rotation angle (degrees) 176.53538416
Shift along axis 9.18353169
> select subtract #20
Nothing selected
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> volume #20 level 0.55
> volume #20 level 0.52
> ui mousemode right zoom
> select add #20
2 models selected
> view sel
> select subtract #20
Nothing selected
> show #!10 models
> hide #!20 models
> show #!20 models
> volume #20 level 0.5
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui tool show "Color Zone"
> color zone #20 near #10 distance 5.7
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!20 models
> show #!20 models
> hide #!10 models
> show #!10 models
> hide #!20 models
> show #!20 models
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_13_mrc1_mcm265_cdc45/fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif
Chain information for fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> ui tool show Matchmaker
> matchmaker #22/B to #10/5 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 5 (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3612.5
RMSD between 349 pruned atom pairs is 0.656 angstroms; (across all 376 pairs:
1.211)
> select add #22
34895 atoms, 35428 bonds, 4406 residues, 1 model selected
> hide sel target a
> cartoon sel
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select subtract #22
Nothing selected
> show #!21 models
> hide #!21 models
> show #!21 models
> fitmap #21 inMap #50
Fit map cryosparc_P17_J819_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 385073 points
correlation = -0.002927, correlation about mean = 0.004409, overlap = -0.0752
steps = 684, shift = 150, angle = 30.2 degrees
Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.57579874 0.59202822 -0.56387799 140.55370059
0.23007257 0.54448263 0.80660106 227.62276282
0.78455237 -0.59417273 0.17730296 170.40181219
Axis -0.70827102 -0.68180470 -0.18301506
Axis point 0.00000000 142.99311800 40.24521085
Rotation angle (degrees) 81.44306259
Shift along axis -285.93048023
> hide #!20 models
> show #!20 models
> lighting simple
> select add #21
3 models selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.97135,-0.052031,-0.23188,161.6,0.15157,0.88715,0.43587,-376.59,0.18303,-0.45853,0.86962,210.47
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.19048,0.81338,-0.54967,226.48,0.29087,0.48802,0.82294,-405.4,0.93761,-0.31663,-0.14363,216.66
> view matrix models
> #21,-0.32552,0.21775,-0.92012,629.77,-0.85556,0.34648,0.38467,69.087,0.40256,0.91244,0.073519,-23.833
> view matrix models
> #21,-0.53454,-0.15623,-0.83058,768.38,-0.79246,0.43422,0.42833,16.109,0.29374,0.88715,-0.35592,123.32
> view matrix models
> #21,-0.53754,0.14132,-0.83131,687.98,-0.53102,0.70909,0.46391,-142.08,0.65503,0.69082,-0.30612,62.244
> view matrix models
> #21,-0.084069,-0.50373,-0.85976,743.6,-0.50818,0.76385,-0.39785,56.165,0.85714,0.40347,-0.3202,87.35
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.084069,-0.50373,-0.85976,600,-0.50818,0.76385,-0.39785,93.73,0.85714,0.40347,-0.3202,23.425
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.11912,-0.5728,-0.81099,616.38,-0.60623,0.68884,-0.39748,141.88,0.78632,0.44429,-0.4293,60.08
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.11912,-0.5728,-0.81099,641.5,-0.60623,0.68884,-0.39748,134.93,0.78632,0.44429,-0.4293,-49.603
> select subtract #21
Nothing selected
> fitmap #21 inMap #50
Fit map cryosparc_P17_J819_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 385073 points
correlation = 0.9655, correlation about mean = 0.736, overlap = 1.153e+06
steps = 428, shift = 23.7, angle = 35.9 degrees
Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
-0.97650910 -0.21085482 -0.04438713 623.66015597
-0.20170409 0.96695488 -0.15592857 100.07508728
0.07579864 -0.14331260 -0.98677052 575.69053694
Axis 0.10409896 -0.99169665 0.07550605
Axis point 308.29085690 0.00000000 301.17618213
Rotation angle (degrees) 176.52597465
Shift along axis 9.14636480
> ui mousemode right zoom
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!20 models
> color #21 #ffffb2b1 models
> color #21 #ffffb2c3 models
> color #21 #ffffb2cd models
> lighting soft
> hide #!21 models
> show #!20 models
> hide #!10 models
> hide #!20 models
> show #!21 models
> color #21 #ffffb2ff models
> volume #21 level 0.3
> show #!10 models
> hide #22 models
> hide #!21 models
> show #!21 models
> volume #21 color #ffffb2a7
> volume #21 color #ffffb2c7
> volume #21 level 0.2436
> lighting simple
> volume #21 level 0.1591
> show #22 models
> volume #21 level 0.1281
> volume #21 level 0.1788
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> select #22/1
Nothing selected
> hide #22 models
> show #22 models
> select #22/A
8735 atoms, 8850 bonds, 1096 residues, 1 model selected
> color sel red
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel fire brick
[Repeated 1 time(s)]
> select clear
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #22 models
> show #22 models
> hide #!21 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> matchmaker #22/E to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
alignment score = 3080.7
RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
1.017)
> show #!21 models
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> color #21 #ffffb2bd models
> color #21 #ffffb2b5 models
> color #21 #ffffb2b2 models
> color #21 #ffffb2b3 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!21 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map.mrc
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.12, step 4, values float32
> select add #23
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,-7.0847,0,1,0,-197.97,0,0,1,-109.28
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.98683,-0.1075,-0.12084,64.211,0.093694,0.98898,-0.11463,-186.41,0.13184,0.1018,0.98603,-171.46
> view matrix models
> #23,0.94591,0.31213,-0.088466,-59.663,-0.29926,0.73415,-0.60948,142.32,-0.12529,0.60298,0.78785,-193.05
> view matrix models
> #23,0.82112,-0.20887,0.53116,-52.333,0.43246,0.83502,-0.34017,-166.12,-0.37248,0.50903,0.77598,-94.238
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.82112,-0.20887,0.53116,-76.409,0.43246,0.83502,-0.34017,-186.01,-0.37248,0.50903,0.77598,-92.077
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.83793,-0.011709,0.54565,-144.2,0.24675,0.89989,-0.35961,-149.17,-0.48681,0.43596,0.75693,-33.526
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.83793,-0.011709,0.54565,-128.24,0.24675,0.89989,-0.35961,-146.49,-0.48681,0.43596,0.75693,-40.894
> fitmap #23 inMap #50
Fit map cryosparc_P17_J842_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 31738 points
correlation = 0.8988, correlation about mean = 0.8848, overlap = 2.616e+04
steps = 240, shift = 14.4, angle = 16.1 degrees
Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.99999950 -0.00093282 -0.00036048 0.38612693
0.00093288 0.99999955 0.00017577 -0.28600473
0.00036032 -0.00017611 0.99999992 -0.03720041
Axis -0.17327202 -0.35493124 0.91869507
Axis point 306.61813627 413.85199204 0.00000000
Rotation angle (degrees) 0.05817852
Shift along axis 0.00043119
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #23 step 1
> select subtract #23
Nothing selected
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> hide #!21 models
> volume #20 level 0.4302
> volume #20 level 0.3778
> volume #20 level 0.35
> color zone #20 near #10 distance 5.7
> color single #20
> color #20 #b2b2b2d5 models
> color #20 #b2b2b2be models
> color #20 #b2b2b2bf models
> hide #!10 models
> show #!10 models
> hide #22 models
> show #22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> fitmap #23 inMap #50
Fit map cryosparc_P17_J842_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 2030930 points
correlation = 0.8962, correlation about mean = 0.8821, overlap = 1.677e+06
steps = 40, shift = 0.0507, angle = 0.0557 degrees
Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
1.00000000 -0.00007868 -0.00004863 0.03041624
0.00007868 0.99999998 -0.00016626 0.01451905
0.00004864 0.00016625 0.99999998 -0.05718112
Axis 0.87385342 -0.25564418 0.41355321
Axis point 0.00000000 342.00873970 86.09530376
Rotation angle (degrees) 0.01090079
Shift along axis -0.00077981
> volume #23 level 0.2075
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!23 models
> show #!21 models
> hide #!23 models
> hide #!21 models
> hide #22 models
> show #22 models
> select clear
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #22 models
> show #!20 models
> hide #!21 models
> volume #20 level 0.38
> volume #20 level 0.4
> volume #20 level 0.45
> show #22 models
> hide #22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #22 models
> hide #22 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> color #23 #b2ffffcc models
> show #22 models
> hide #22 models
> show #22 models
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #22 models
> show #22 models
> hide #22 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> ui mousemode right zoom
> hide #!23 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J1282_volume_map.mrc
Opened cryosparc_P17_J1282_volume_map.mrc as #24, grid size 588,588,588, pixel
0.95, shown at level 0.156, step 4, values float32
> close #24
> show #22 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #22 models
> show #22 models
> matchmaker #22/B to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3101.9
RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
7.919)
> matchmaker #22/C to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain C (#22), sequence
alignment score = 468.1
RMSD between 6 pruned atom pairs is 1.308 angstroms; (across all 25 pairs:
19.655)
> hide #22 models
> show #22 models
> matchmaker #22/B to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3101.9
RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
7.919)
> hide #!23 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> matchmaker #22/E to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
alignment score = 3080.7
RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
1.017)
> matchmaker #22/B to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3481.1
RMSD between 244 pruned atom pairs is 0.690 angstroms; (across all 293 pairs:
3.338)
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> volume #23 level 0.18
> hide #22 models
> show #22 models
> hide #22 models
> show #!21 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> volume #21 level 0.16
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #22 models
> show #22 models
> hide #!21 models
> hide #!23 models
> hide #22 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif
Chain information for
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif #24
---
Chain | Description
A | .
B | .
C | .
D E | .
F G | .
H I J | .
K | .
> select add #24
34488 atoms, 35097 bonds, 4327 residues, 1 model selected
> hide sel target a
> cartoon sel
> select subtract #24
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #24/B to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain B
(#24), sequence alignment score = 3082.5
RMSD between 545 pruned atom pairs is 0.663 angstroms; (across all 564 pairs:
0.931)
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> matchmaker #24/C to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain C
(#24), sequence alignment score = 3488.9
RMSD between 245 pruned atom pairs is 0.669 angstroms; (across all 293 pairs:
1.945)
> select #24/A
1510 atoms, 1527 bonds, 185 residues, 1 model selected
> color sel red
> select #10/M:96
22 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> color #10,24 hot pink
> undo
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel hot pink
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> color sel blue violet
> color sel orchid
> color sel deep pink
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel medium violet red
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel magenta
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel dark orchid
> select clear
> show #22 models
> hide #22 models
> show #22 models
> hide #24 models
> hide #22 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #!10 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> select #24/D,E
2164 atoms, 2190 bonds, 272 residues, 1 model selected
> color sel dodger blue
> color sel steel blue
> color sel dodger blue
> select clear
> show #!10 models
> select #24/K
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> select clear
> select #24/K
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> color sel yellow green
> color sel orange
> select clear
[Repeated 1 time(s)]
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!10 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
Chain information for fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
#25
---
Chain | Description
A | .
B | .
C | .
D E F | .
G | .
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> select add #25
30722 atoms, 31289 bonds, 3849 residues, 1 model selected
> select subtract #25
Nothing selected
> select add #25
30722 atoms, 31289 bonds, 3849 residues, 1 model selected
> hide sel target a
> cartoon sel
> select subtract #25
Nothing selected
> matchmaker #25/B to #24/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
chain B (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
chain B (#25), sequence alignment score = 3315.9
RMSD between 585 pruned atom pairs is 0.430 angstroms; (across all 650 pairs:
3.003)
> hide #!10 models
> matchmaker #25/C to #24/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
chain C (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
chain C (#25), sequence alignment score = 4205.3
RMSD between 670 pruned atom pairs is 0.557 angstroms; (across all 868 pairs:
28.308)
> hide #24 models
> show #24 models
> hide #24 models
> select #25/A
1510 atoms, 1527 bonds, 185 residues, 1 model selected
> color sel red
> color sel orange red
> select clear
> show #24 models
> select #25/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> select #25/G
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> color sel coral
> color sel sienna
> select clear
[Repeated 1 time(s)]
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #25 models
> select #24/H,I,J
10980 atoms, 11241 bonds, 1371 residues, 1 model selected
> color sel slate gray
> color sel cadet blue
> select add #24
34488 atoms, 35097 bonds, 4327 residues, 1 model selected
> select subtract #24
Nothing selected
> hide #24 models
> show #24 models
> hide #24 models
> show #25 models
> select #25/D,E,F
10980 atoms, 11241 bonds, 1371 residues, 1 model selected
> color sel medium aquamarine
> color sel cyan
> select clear
> show #24 models
> show #!10 models
> hide #25 models
> hide #24 models
> hide #!10 models
> show #24 models
> show #25 models
> hide #25 models
> show #25 models
> hide #24 models
> show #!10 models
> hide #!10 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> hide #24 models
> hide #25 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_323_337_tof1_model_0.cif
Chain information for fold_mrc1_323_337_tof1_model_0.cif #26
---
Chain | Description
A | .
B | .
> select #26/B
9945 atoms, 10133 bonds, 1238 residues, 1 model selected
> color sel slate blue
> color sel medium slate blue
[Repeated 4 time(s)]
> color sel dark slate blue
[Repeated 1 time(s)]
> color sel rebecca purple
[Repeated 4 time(s)]
> select clear
> show #!10 models
> matchmaker #26/B to #10/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain X (#10) with
fold_mrc1_323_337_tof1_model_0.cif, chain B (#26), sequence alignment score =
5350.8
RMSD between 514 pruned atom pairs is 0.989 angstroms; (across all 665 pairs:
3.879)
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif
Chain information for fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif #27
---
Chain | Description
A | .
B | .
C | .
D | .
> matchmaker #27/B to #10/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain X (#10) with
fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif, chain B (#27), sequence
alignment score = 5344.2
RMSD between 523 pruned atom pairs is 0.976 angstroms; (across all 665 pairs:
3.339)
> select #27/B
9945 atoms, 10133 bonds, 1238 residues, 1 model selected
> color sel blue violet
> select #27/A
201 atoms, 202 bonds, 24 residues, 1 model selected
> color sel red
> select #27/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel orchid
> color sel medium orchid
[Repeated 1 time(s)]
> color sel dark orchid
> color sel medium orchid
> select clear
> select #27/D
7928 atoms, 8057 bonds, 1017 residues, 1 model selected
> color sel light coral
> select clear
> hide #26 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_385_456_mcm6_model_0.cif
Chain information for fold_mrc1_385_456_mcm6_model_0.cif #28
---
Chain | Description
A | .
B | .
> hide #27 models
> hide #28 models
> show #28 models
> select #28/A
560 atoms, 562 bonds, 72 residues, 1 model selected
> color sel red
> select clear
> matchmaker #28/B to #10/AB pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AB (#10) with
fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
4104.2
RMSD between 300 pruned atom pairs is 0.858 angstroms; (across all 332 pairs:
2.385)
> hide #28 models
> show #28 models
> hide #!10 models
> show #!10 models
> matchmaker #28/B to #10/8 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 8 (#10) with
fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
4030.4
RMSD between 253 pruned atom pairs is 0.826 angstroms; (across all 305 pairs:
2.667)
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #28/A
560 atoms, 562 bonds, 72 residues, 1 model selected
> color sel dark red
> select #28/B
7928 atoms, 8057 bonds, 1017 residues, 1 model selected
> color sel orange
> select clear
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_813_865_mcm2_cdc45_model_0.cif
Chain information for fold_mrc1_813_865_mcm2_cdc45_model_0.cif #29
---
Chain | Description
A | .
B | .
C | .
> select #29/A
445 atoms, 451 bonds, 53 residues, 1 model selected
> color sel red
> select clear
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel pale violet red
> select clear
> matchmaker #29/B to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B (#29), sequence alignment
score = 13
Fewer than 3 residues aligned; cannot match extended_structure, chain 2 with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> select #29/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> matchmaker #29/C to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain C (#29), sequence alignment
score = 3493.1
RMSD between 246 pruned atom pairs is 0.605 angstroms; (across all 293 pairs:
1.580)
> color sel pale violet red
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel gray
[Repeated 5 time(s)]
> color sel light gray
> color sel gray
> color sel light yellow
[Repeated 1 time(s)]
> color sel old lace
[Repeated 1 time(s)]
> color sel antique white
[Repeated 1 time(s)]
> color sel ghost white
> color sel mint cream
> color sel white smoke
[Repeated 1 time(s)]
> color sel beige
[Repeated 1 time(s)]
> color sel azure
> color sel wheat
[Repeated 1 time(s)]
> select clear
> hide #28 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_908_925_cdc45_model_0.cif
Chain information for fold_mrc1_908_925_cdc45_model_0.cif #30
---
Chain | Description
A | .
B | .
> select #30/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel lavender
> color sel gainsboro
> color sel dim gray
> color sel gray
> color sel light gray
> color sel thistle
[Repeated 1 time(s)]
> select #30/A
145 atoms, 146 bonds, 18 residues, 1 model selected
> color sel red
> select clear
> matchmaker #30/B to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_mrc1_908_925_cdc45_model_0.cif, chain B (#30), sequence alignment score =
3073.5
RMSD between 536 pruned atom pairs is 0.657 angstroms; (across all 564 pairs:
1.134)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Mon Sep 16 15:36:42 2024 \u2014\u2014\u2014
opened ChimeraX session
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif #31
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif #32
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif #33
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> hide #30 models
> hide #32 models
> hide #33 models
> hide #31 models
> show #31 models
> ui tool show Matchmaker
> matchmaker #31/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif, chain A (#31),
sequence alignment score = 3496.1
RMSD between 253 pruned atom pairs is 0.662 angstroms; (across all 293 pairs:
1.847)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #31
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> show #32 models
> show #33 models
> select add #32
75104 atoms, 76324 bonds, 9428 residues, 2 models selected
> select add #33
112656 atoms, 114486 bonds, 14142 residues, 3 models selected
> hide sel target a
> cartoon sel
> select subtract #33
75104 atoms, 76324 bonds, 9428 residues, 2 models selected
> select subtract #32
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> select subtract #31
Nothing selected
> hide #32 models
> hide #33 models
> show #32 models
> show #33 models
> select #31/A #32/A #33/A
20814 atoms, 21141 bonds, 2604 residues, 3 models selected
> color sel hot pink
> select #31/B #32/B #33/B
7806 atoms, 7926 bonds, 1002 residues, 3 models selected
> color sel yellow
> select #31/C #32/C #33/C
23784 atoms, 24171 bonds, 3051 residues, 3 models selected
> color sel orange
> select #31/D #32/D #33/D
15693 atoms, 15963 bonds, 1950 residues, 3 models selected
> color sel light gray
> select #31/E #32/E #33/E
29835 atoms, 30399 bonds, 3714 residues, 3 models selected
> ui tool show "Color Actions"
> color sel slate blue
> select #31/F #32/F #33/F
14724 atoms, 14886 bonds, 1821 residues, 3 models selected
> color sel red
> select add #31
47368 atoms, 48086 bonds, 5928 residues, 3 models selected
> select add #32
80012 atoms, 81286 bonds, 10035 residues, 3 models selected
> select subtract #31
42460 atoms, 43124 bonds, 5321 residues, 2 models selected
> select subtract #32
4908 atoms, 4962 bonds, 607 residues, 1 model selected
> select add #33
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> select subtract #33
Nothing selected
> select clear
> matchmaker #32/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif, chain A (#32),
sequence alignment score = 3505.1
RMSD between 253 pruned atom pairs is 0.693 angstroms; (across all 293 pairs:
1.550)
> matchmaker #33/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif, chain A (#33),
sequence alignment score = 3502.1
RMSD between 258 pruned atom pairs is 0.659 angstroms; (across all 293 pairs:
1.500)
> lighting simple
> hide #32 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #32 models
> hide #32 models
> show #32 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> hide #!10 models
> show #!50 models
> hide #!50 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Tue Sep 24 13:00:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> lighting simple
> open /Users/cvetkom/Documents/pdb/4c95_Ctf4_Sld5.pdb
4c95_Ctf4_Sld5.pdb title:
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to SLD5
[more info...]
Chain information for 4c95_Ctf4_Sld5.pdb #34
---
Chain | Description
A B C | No description available
D E | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #34
9660 atoms, 9722 bonds, 4 pseudobonds, 1360 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #34
Nothing selected
> select #34/A
3494 atoms, 3493 bonds, 2 pseudobonds, 510 residues, 2 models selected
> select #34/B
3531 atoms, 3550 bonds, 1 pseudobond, 498 residues, 2 models selected
> select #34/C
2427 atoms, 2473 bonds, 1 pseudobond, 326 residues, 2 models selected
> select #34/D
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/E
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/D,E
208 atoms, 206 bonds, 26 residues, 1 model selected
> color sel red
> hide #31 models
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_3c_ctf4_mrc1_1081_1096/fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif
Chain information for fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif #35
---
Chain | Description
A B C | .
D | .
> show #!10 models
> hide #!23 models
> select clear
> ui tool show Matchmaker
> matchmaker #34/B to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with 4c95_Ctf4_Sld5.pdb, chain B
(#34), sequence alignment score = 2232.7
RMSD between 391 pruned atom pairs is 0.878 angstroms; (across all 424 pairs:
1.248)
> matchmaker #35/A to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with
fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif, chain A (#35), sequence
alignment score = 2301.6
RMSD between 411 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.817)
> hide #!10 models
> show #!10 models
> show #!23 models
> hide #!23 models
> show #!42 models
> color #42 #b2b2ffeb models
> color #42 #b2b2ffff models
> color #42 #b2b2ffb7 models
> color #42 #b2b2ff95 models
> color #42 #b2b2ff84 models
> hide #!10 models
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> hide #!42 models
> show #!42 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #35 models
> show #35 models
> hide #!42 models
> show #!42 models
> hide #35 models
> show #35 models
> select #35/D
128 atoms, 129 bonds, 16 residues, 1 model selected
> color sel orange
> color sel orange red
> color sel orange
> select clear
> hide #!34 models
> show #!34 models
> ui tool show "Fit in Map"
> hide #!42 models
> show #!42 models
> fitmap #34 inMap #42
Fit molecule 4c95_Ctf4_Sld5.pdb (#34) to map sharpened_replisome.mrc copy
(#42) using 9660 atoms
average map value = 0.381, steps = 128
shifted from previous position = 2.63
rotated from previous position = 6.17 degrees
atoms outside contour = 4354, contour level = 0.3
Position of 4c95_Ctf4_Sld5.pdb (#34) relative to sharpened_replisome.mrc copy
(#42) coordinates:
Matrix rotation and translation
0.28572805 -0.31647925 0.90454429 338.42345045
-0.43402411 -0.88427381 -0.17228725 294.11719747
0.85439016 -0.34336673 -0.39002146 373.35631167
Axis -0.80114939 0.23486712 -0.55045172
Axis point 0.00000000 201.64420355 57.39058667
Rotation angle (degrees) 173.87077288
Shift along axis -407.56390486
> fitmap #35 inMap #42
Fit molecule fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) to map
sharpened_replisome.mrc copy (#42) using 11336 atoms
average map value = 0.4111, steps = 68
shifted from previous position = 0.628
rotated from previous position = 1.83 degrees
atoms outside contour = 4371, contour level = 0.3
Position of fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) relative
to sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
-0.98706242 -0.07882972 0.13961966 285.86123137
0.08488406 0.48183004 0.87214363 299.11678968
-0.13602378 0.87271169 -0.46890494 372.10103280
Axis 0.00177188 0.85978425 0.51065438
Axis point 149.35362784 0.00000000 83.84935178
Rotation angle (degrees) 170.77580491
Shift along axis 447.69744149
> hide #35 models
> hide #!42 models
> show #!42 models
> hide #!34 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> hide #!42 models
> show #!42 models
> color #42 #b2b2ffff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!47 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> hide #!42 models
> hide #!46 models
> show #!43 models
> hide #!43 models
> show #!34 models
> show #33 models
> hide #33 models
> show #35 models
> hide #!34 models
> show #!34 models
> hide #35 models
> show #35 models
> show #!2 models
> hide #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Wed Sep 25 19:02:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!34 models
> hide #35 models
> show #35 models
> hide #35 models
> close #2-3
> close #7
> close #11
> close #9
> show #!50 models
> hide #!50 models
> show #!53 models
> close #53
> show #!52 models
> close #52
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!10 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
\u2014\u2014\u2014 End of log from Fri Oct 4 13:17:26 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_EMready.mrc
Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
588,588,588, pixel 0.95, shown at level 0.0383, step 4, values float32
> volume #2 step 1
> volume #2 level 0.9283
> volume #2 level 1.647
> ui tool show "Side View"
> hide #!2 models
> show #!21 models
> show #!2 models
> select add #2
2 models selected
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.21372,0.65189,-0.72758,228.01,-0.15215,0.75791,0.63437,-52.313,0.96497,-0.024879,0.26116,-76.828
> view matrix models
> #2,-0.22904,0.42092,-0.8777,455.06,-0.48229,0.73415,0.47793,87.401,0.84554,0.53277,0.034859,-139.12
> view matrix models
> #2,-0.30253,0.24312,-0.92161,536.06,-0.68897,0.61238,0.38771,202.38,0.65863,0.75225,-0.017761,-133.46
> view matrix models
> #2,-0.17917,0.019523,-0.98362,578.75,-0.64564,0.75206,0.13253,216.8,0.74233,0.65881,-0.12214,-104.65
> view matrix models
> #2,-0.39996,0.21624,-0.89066,563.08,-0.18128,0.93391,0.30815,-9.3049,0.89843,0.28471,-0.33432,8.6733
> view matrix models
> #2,-0.45252,0.485,-0.74833,467.43,0.38691,0.86285,0.32525,-154.48,0.80345,-0.14235,-0.57811,215.56
> view matrix models
> #2,-0.19899,0.25008,-0.94756,511.54,0.14679,0.96359,0.22349,-88.484,0.96895,-0.094621,-0.22845,66.354
> view matrix models
> #2,-0.40366,0.20697,-0.89119,566.81,-0.0090314,0.97313,0.23009,-48.812,0.91486,0.10093,-0.39095,69.189
> view matrix models
> #2,-0.42359,0.12332,-0.89742,597.11,0.0008642,0.99074,0.13574,-32.363,0.90585,0.056721,-0.41978,91.291
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.42359,0.12332,-0.89742,572.5,0.0008642,0.99074,0.13574,-244.94,0.90585,0.056721,-0.41978,20.155
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.42268,0.11844,-0.8985,573.87,0.0011522,0.99149,0.13015,-243.8,0.90628,0.053978,-0.41923,20.651
> view matrix models
> #2,-0.54332,-0.16268,-0.82361,666.33,-0.42868,0.89727,0.10557,-90.185,0.72182,0.41043,-0.55725,9.6598
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,654.96,-0.41205,0.88859,0.20156,-117.01,0.6926,0.44919,-0.56439,9.0402
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,657.43,-0.41205,0.88859,0.20156,-126.64,0.6926,0.44919,-0.56439,12.296
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,663.52,-0.41205,0.88859,0.20156,-124.44,0.6926,0.44919,-0.56439,2.3033
> ui mousemode right zoom
> ui tool show "Fit in Map"
> fitmap #2 inMap #21
Fit map cryosparc_P17_J819_005_volume_map_EMready.mrc in map
cryosparc_P17_J819_005_volume_map.mrc using 740829 points
correlation = 0.938, correlation about mean = 0.7691, overlap = 1.576e+06
steps = 160, shift = 3.85, angle = 10.8 degrees
Position of cryosparc_P17_J819_005_volume_map_EMready.mrc (#2) relative to
cryosparc_P17_J819_005_volume_map.mrc (#21) coordinates:
Matrix rotation and translation
0.99999999 0.00005310 -0.00009395 0.01216343
-0.00005312 0.99999998 -0.00020453 0.08100750
0.00009394 0.00020453 0.99999998 -0.07859161
Axis 0.88443714 -0.40622568 -0.22967726
Axis point 0.00000000 388.90207101 387.88928499
Rotation angle (degrees) 0.01324986
Shift along axis -0.00409883
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!20 models
> show #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> volume #3 step 1
> volume #3 level 0.2175
> volume #3 level 0.4032
> select add #3
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96087,0.15628,0.2287,-100.29,-0.086083,0.95323,-0.28971,123.99,-0.26328,0.25869,0.92939,24.765
> view matrix models
> #3,0.94784,0.022072,0.31799,-87.222,0.026112,0.98887,-0.14647,39.853,-0.31769,0.14713,0.93671,67.954
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.94784,0.022072,0.31799,-188.13,0.026112,0.98887,-0.14647,-129.94,-0.31769,0.14713,0.93671,62.858
> view matrix models
> #3,0.94784,0.022072,0.31799,-118.63,0.026112,0.98887,-0.14647,-168.34,-0.31769,0.14713,0.93671,-44.135
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-179.94,0.1255,0.94252,-0.30967,-134.37,-0.59565,0.32121,0.73623,46.771
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-166.19,0.1255,0.94252,-0.30967,-142.23,-0.59565,0.32121,0.73623,35.37
> view matrix models
> #3,0.79338,0.092061,0.60172,-165.26,0.1255,0.94252,-0.30967,-141.13,-0.59565,0.32121,0.73623,35.671
> select subtract #3
Nothing selected
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 329084 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.568e+05
steps = 236, shift = 0.4, angle = 16.9 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 -0.00001351 0.00004557 -0.02152036
0.00001352 1.00000000 -0.00003397 0.01017840
-0.00004557 0.00003397 1.00000000 0.00711885
Axis 0.58150158 0.77996616 0.23131947
Axis point 171.08172050 0.00000000 434.91154679
Rotation angle (degrees) 0.00334730
Shift along axis -0.00292859
> hide #!42 models
> show #!42 models
> volume #3 level 0.3
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> ui mousemode right zoom
> ui tool show "Hide Dust"
> surface undust #42
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 586182 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.874e+05
steps = 28, shift = 0.0238, angle = 0.00733 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 0.00000906 -0.00005933 0.02130757
-0.00000906 1.00000000 0.00003559 -0.01782195
0.00005933 -0.00003559 1.00000000 0.00029158
Axis -0.51008916 -0.85026779 -0.12982191
Axis point -14.19118466 0.00000000 395.65343560
Rotation angle (degrees) 0.00399795
Shift along axis 0.00424682
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
480,480,480, pixel 0.95, shown at level 0.152, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.95, shown at level 0.28, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
480,480,480, pixel 0.95, shown at level 0.569, step 2, values float32
> volume #11 level 2.423
> volume #9 level 0.9574
> volume #11 step 1
> volume #9 step 1
> volume #7 step 1
> volume #7 level 0.2399
> select add #7
2 models selected
> select add #9
4 models selected
> select add #11
6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#9,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#11,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2
> view matrix models
> #7,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#9,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#11,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885
> view matrix models
> #7,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#9,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#11,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14
> view matrix models
> #7,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#9,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#11,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79
> view matrix models
> #7,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#9,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#11,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21
> view matrix models
> #7,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#9,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#11,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05
> view matrix models
> #7,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#9,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#11,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39
> view matrix models
> #7,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#9,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#11,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06
> view matrix models
> #7,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#9,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#11,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57
> view matrix models
> #7,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#9,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#11,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6
> view matrix models
> #7,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#9,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#11,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#9,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#11,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#9,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#11,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2
> view matrix models
> #7,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#9,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#11,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#9,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#11,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52
> view matrix models
> #7,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#9,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#11,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#9,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#11,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51
> view matrix models
> #7,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#9,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#11,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95
> view matrix models
> #7,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#9,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#11,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87
> view matrix models
> #7,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#9,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#11,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3
> view matrix models
> #7,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#9,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#11,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!23 models
> hide #!23 models
> show #!23 models
> fitmap #7 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 611645 points
correlation = 0.8586, correlation about mean = 0.4556, overlap = 8.71e+04
steps = 244, shift = 17, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map.mrc (#7) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55644781 -0.77930109 0.28819374 245.87868586
-0.75685869 -0.33229301 0.56280215 362.24414012
-0.34282757 -0.53129197 -0.77472452 653.58997201
Axis -0.86611289 0.49953261 0.01776598
Axis point 0.00000000 386.34237031 252.82329186
Rotation angle (degrees) 140.83086649
Shift along axis -20.39427278
> hide #!7 models
> show #!7 models
> fitmap #9 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 166113 points
correlation = 0.8354, correlation about mean = 0.2023, overlap = 1.093e+05
steps = 240, shift = 17.3, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc (#9) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55535502 -0.78023657 0.28777020 246.41094031
-0.75768547 -0.33209636 0.56180488 362.67622759
-0.34277328 -0.53004046 -0.77560530 653.54700022
Axis -0.86582981 0.50001893 0.01788295
Axis point 0.00000000 386.54023823 252.88749245
Rotation angle (degrees) 140.91153143
Shift along axis -20.31760982
> fitmap #11 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 547647 points
correlation = 0.755, correlation about mean = 0.2272, overlap = 1.157e+06
steps = 244, shift = 16, angle = 22.6 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc (#11) relative
to cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55439930 -0.78039733 0.28917368 246.34842101
-0.75807382 -0.33013049 0.56243927 362.20292573
-0.34346106 -0.53103093 -0.77462290 653.67877730
Axis -0.86543769 0.50070495 0.01766816
Axis point 0.00000000 386.83809960 252.79416826
Rotation angle (degrees) 140.82108735
Shift along axis -20.29310612
> ui mousemode right zoom
> select subtract #7
4 models selected
> select subtract #9
2 models selected
> select subtract #11
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #9 level 0.7158
> volume #9 level 0.7
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.4
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!9 models
> show #!9 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #26 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!50 models
> hide #!9 models
> hide #!50 models
> show #!50 models
> color #50 #b2b2b29c models
> volume #50 level 3
> volume #50 level 3.5
> volume #50 level 3.6
> volume #50 level 3.8
> volume #50 level 4.5
> show #!42 models
> hide #!50 models
> hide #!42 models
> show #!3 models
> select add #3
2 models selected
> color #3.1 gray
> ui tool show "Color Actions"
> color sel light blue
> color sel light sky blue
> color sel aquamarine
> color sel light sky blue
> select subtract #3
Nothing selected
> color #3 #87cefaa8 models
> color #3 #87cefa98 models
> color #3 #87cefaa7 models
> color #3 #87cefa99 models
> color #3 #87cefaa4 models
> color #3 #87cefaa3 models
> volume #3 level 0.35
> fitmap #26 inMap #3
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) using 10075 atoms
average map value = 0.2438, steps = 52
shifted from previous position = 0.293
rotated from previous position = 0.36 degrees
atoms outside contour = 7077, contour level = 0.35
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.84462737 0.15456521 -0.51255653 282.60576624
0.06681694 0.91949322 0.38738573 335.32756599
0.53116861 -0.36144406 0.76630157 241.89923621
Axis -0.58158875 -0.81062320 -0.06815088
Axis point -335.92841792 0.00000000 139.55904352
Rotation angle (degrees) 40.07422511
Shift along axis -452.67028623
> volume #3 level 0.34
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_sharp_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> ui tool show "Side View"
> rock y 20 136
> volume #3 level 0.32
> volume #3 level 0.33
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
> hide #!3 models
> show #!50 models
> volume #50 level 5
> volume #50 level 4.6
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
No frames have been recorded
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
> fitmap #26 inMap #50
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
J842_005_volume_map_EMReady.mrc (#50) using 10075 atoms
average map value = 2.525, steps = 52
shifted from previous position = 0.107
rotated from previous position = 0.359 degrees
atoms outside contour = 7517, contour level = 4.6
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.84685173 0.15716115 -0.50807727 282.58642125
0.06188411 0.91973007 0.38764280 335.21799844
0.52821633 -0.35971789 0.76914923 241.85487927
Axis -0.58331859 -0.80883211 -0.07436418
Axis point -334.58664400 0.00000000 135.85619956
Rotation angle (degrees) 39.83740038
Shift along axis -453.95833613
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_EMReady_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> select add #26
10075 atoms, 10266 bonds, 1253 residues, 1 model selected
> cartoon hide sel
> show sel target ab
> style sel ball
Changed 10075 atom styles
> color sel byhetero
> select clear
> cartoon #26,50
> hide #26,50 target a
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #26 models
> show #26 models
> hide #!50 models
> show #!11 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!7 models
> hide #!11 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
2 models selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel light sea green
> color #7 #b2ffff9d models
> color #7 #b2ffffd9 models
> color #7 #b2ffffb7 models
> color #7 #b2ffffa7 models
> color #7 #b2ffffa6 models
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> volume #7 level 0.22
> volume #7 level 0.2
> volume #7 level 0.18
> volume #7 level 0.16
> volume #7 level 0.18
> volume #7 level 0.2
> volume #7 level 0.18
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 4.6, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
588,588,588, pixel 0.95, shown at level 1.65, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
480,480,480, pixel 0.95, shown at level 0.18, step 1, values float32
Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.95, shown at level 0.7, step 1, values float32
Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
480,480,480, pixel 0.95, shown at level 2.42, step 1, values float32
Log from Mon Oct 7 10:20:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Fri Oct 4 13:17:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Wed Sep 25 19:02:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Tue Sep 24 13:00:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32
Log from Mon Sep 16 15:36:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Wed Sep 11 12:56:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Mon Sep 9 04:24:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32
Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Log from Fri Sep 6 19:48:00 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Log from Fri Sep 6 19:04:03 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.227, step 1, values float32
Log from Fri Sep 6 16:21:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
Log from Wed Sep 4 08:32:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Log from Wed Sep 4 05:32:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 1, values float32
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at level 0.02, step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
Log from Tue Sep 3 13:30:10 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
pixel 1.9, shown at level 0.362, step 2, values float32
Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
pixel 1.9, shown at level 0.34, step 1, values float32
Log from Tue Jul 30 11:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Log from Wed Jul 24 16:21:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
Log from Thu Jul 18 19:11:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 1, values float32
Log from Thu Jul 18 17:16:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.384, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.351, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.329, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.392, step 1, values float32
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.226, step 1, values float32
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.247, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 0.998, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.31, step 1, values float32
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.301, step 1, values float32
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.1, step 1, values float32
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.196, step 1, values float32
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.0845, step 1, values float32
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 1, values float32
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.333, step 1, values float32
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.08, step 1, values float32
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.15, step 1, values float32
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 1, values float32
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 1, values float32
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.151, step 1, values float32
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.33, step 1, values float32
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.0045, step 1, values float32
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 1, step 1, values float32
Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
pixel 0.95, shown at level 0.0045, step 1, values float32
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.426, step 2, values float32
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 1, values float32
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 1, values float32
Log from Thu Jul 11 13:31:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 1, values float32
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 1, values float32
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.314, step 1, values float32
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.294, step 1, values float32
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
128,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 1, values float32
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.4, step 1, values float32
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.359, step 1, values float32
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 1, values float32
Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
pixel 1.9, shown at level 0.2, step 1, values float32
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 1, values float32
Log from Fri Jun 21 11:35:11 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
Log from Tue Jun 11 16:35:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0185, step 1, values float32
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 1, values float32
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 1, values float32
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 1, values float32
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.45, step 1, values float32
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 1, values float32
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.32, step 1, values float32
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.25, step 1, values float32
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1, step 1, values float32
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 1, values float32
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.012, step 1, values float32
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 1, values float32
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
Log from Mon Jun 3 09:50:12 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class001.mrc
Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.0106, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class002.mrc
Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class003.mrc
Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.0124, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class004.mrc
Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.0133, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class005.mrc
Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class006.mrc
Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class001.mrc
Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class002.mrc
Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
1.9, shown at level 0.0105, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class003.mrc
Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class004.mrc
Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class005.mrc
Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
1.9, shown at level 0.0142, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class006.mrc
Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
1.9, shown at level 0.0149, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class001.mrc
Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
1.9, shown at level 0.0144, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class002.mrc
Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class003.mrc
Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class004.mrc
Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class005.mrc
Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
1.9, shown at level 0.0143, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class006.mrc
Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> volume all step 1
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job417_run_class001.mrc
Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
shown at level 0.0163, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job423.mrc
Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
shown at level 0.0162, step 2, values float32
> hide #!19 models
> volume #19 step 1
> volume #20 step 1
> hide #!20 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc
Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
294,294,294, pixel 1.9, shown at level 0.362, step 2, values float32
> volume #21 step 1
> volume #21 level 0.4566
> volume #21 level 0.421
> volume #21 level 0.4151
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!15 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!15 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!7 models
> show #!9 models
> volume #7 level 0.01497
> volume #9 level 0.01231
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!12 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class001.mrc
Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
1.9, shown at level 0.0146, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class002.mrc
Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
1.9, shown at level 0.0139, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class003.mrc
Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class004.mrc
Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class005.mrc
Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class006.mrc
Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
1.9, shown at level 0.0181, step 2, values float32
> hide #!7 models
> hide #!9 models
> hide #!11 models
> hide #!12 models
> volume all step 1
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> volume #22 level 0.01345
> volume #22 level 0.0119
> volume #23 level 0.01121
> volume #24 level 0.01399
> volume #24 level 0.01119
> volume #24 level 0.01287
> volume #25 level 0.01349
> hide #!25 models
> show #!26 models
> volume #26 level 0.01133
> hide #!26 models
> show #!27 models
> volume #27 level 0.01296
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> volume #4 level 0.01157
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class001.mrc
Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class002.mrc
Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class003.mrc
Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
1.9, shown at level 0.0194, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class004.mrc
Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class001.mrc
Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class002.mrc
Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class003.mrc
Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class004.mrc
Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
1.9, shown at level 0.0189, step 2, values float32
> volume all step 1
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> volume #28 level 0.01275
> volume #28 level 0.01205
> volume #28 level 0.01231
> volume #29 level 0.01315
> volume #29 level 0.013
> volume #30 level 0.01741
> volume #31 level 0.01451
> volume #31 level 0.01487
> volume #32 level 0.01315
> volume #33 level 0.01302
> volume #34 level 0.01352
> volume #35 level 0.01616
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class001.mrc
Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class002.mrc
Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
1.9, shown at level 0.0162, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class003.mrc
Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class001.mrc
Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class002.mrc
Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
1.9, shown at level 0.0162, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class003.mrc
Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
1.9, shown at level 0.0152, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class004.mrc
Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
1.9, shown at level 0.0168, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class005.mrc
Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class001.mrc
Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class002.mrc
Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
1.9, shown at level 0.0187, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class003.mrc
Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class004.mrc
Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
1.9, shown at level 0.016, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class005.mrc
Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class006.mrc
Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> volume all step 1
> hide #!49 models
> hide #!48 models
> hide #!47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #!42 models
> hide #!41 models
> hide #!40 models
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> show #!37 models
> show #!38 models
> volume #36 level 0.013
> volume #37 level 0.013
> volume #38 level 0.013
> volume #39 level 0.013
> volume #40 level 0.013
> hide #!40 models
> show #!41 models
> volume #41 level 0.013
> show #!40 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!42 models
> volume #42 level 0.013
> hide #!42 models
> show #!43 models
> volume #43 level 0.013
> volume #43 level 0.012
> volume #44 level 0.013
> volume #45 level 0.013
> volume #46 level 0.013
> volume #47 level 0.013
> volume #48 level 0.013
> volume #49 level 0.013
> show #!44 models
> hide #!49 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> hide #!48 models
> show #!49 models
> hide #!49 models
> show #!48 models
> hide #!48 models
> hide #!44 models
> show #!43 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!43 models
> hide #!42 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!38 models
> hide #!38 models
> hide #!39 models
> show #!49 models
> hide #!49 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class001.mrc
Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class002.mrc
Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class003.mrc
Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
1.9, shown at level 0.0189, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class001.mrc
Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
1.9, shown at level 0.0193, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class002.mrc
Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class003.mrc
Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> hide #!51 models
> hide #!52 models
> hide #!53 models
> hide #!54 models
> hide #!55 models
> volume #50 level 0.013
> show #!51 models
> volume #51 level 0.013
> volume all level 0.013
> hide #!51 models
> hide #!50 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!50 models
> show #!51 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!51 models
> hide #!50 models
> hide #!52 models
> show #!51 models
> show #!50 models
> hide #!51 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> volume #50 level 0.012
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> ui tool show "Fit in Map"
> fitmap #50 inMap #15
Fit map Cl3D_job542_run_it025_class001.mrc in map
Cl3D_job411_run_it025_class003.mrc using 342972 points
correlation = 0.9888, correlation about mean = 0.813, overlap = 133.4
steps = 68, shift = 1.95, angle = 0.993 degrees
Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
Cl3D_job411_run_it025_class003.mrc (#15) coordinates:
Matrix rotation and translation
0.99987080 0.01439337 0.00715694 -5.19984751
-0.01434662 0.99987569 -0.00654060 6.68005810
-0.00725019 0.00643707 0.99995300 -1.28059948
Axis 0.37432567 0.41555671 -0.82897100
Axis point 407.25464445 414.10389399 0.00000000
Rotation angle (degrees) 0.99325686
Shift along axis 1.89108642
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!54 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> volume #54 level 0.012
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> fitmap #50 inMap #54
Fit map Cl3D_job542_run_it025_class001.mrc in map
Cl3D_job545_run_it025_class002.mrc using 342972 points
correlation = 0.9989, correlation about mean = 0.9796, overlap = 133
steps = 56, shift = 2.3, angle = 1.62 degrees
Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
Cl3D_job545_run_it025_class002.mrc (#54) coordinates:
Matrix rotation and translation
0.99982077 -0.01310087 0.01366700 -0.20479433
0.01319269 0.99989086 -0.00664955 -1.77455886
-0.01357839 0.00682866 0.99988449 1.74879695
Axis 0.33535327 0.67789597 0.65421345
Axis point 134.82260247 0.00000000 13.62266755
Rotation angle (degrees) 1.15146770
Shift along axis -0.12755828
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> hide #!50 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class001.mrc
Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class002.mrc
Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class003.mrc
Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
1.9, shown at level 0.0184, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class001.mrc
Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class002.mrc
Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class003.mrc
Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class004.mrc
Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> volume all step 1
> volume all level 0.013
> hide #!57 models
> hide #!58 models
> hide #!59 models
> hide #!60 models
> hide #!61 models
> hide #!62 models
> show #!57 models
> hide #!56 models
> show #!58 models
> hide #!57 models
> volume #58 level 0.01852
> hide #!58 models
> show #!57 models
> hide #!57 models
> show #!56 models
> volume #56 level 0.012
> hide #!56 models
> show #!59 models
> volume #59 level 0.012
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> show #!59 models
> hide #!59 models
> volume #62 level 0.012
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!61 models
> hide #!61 models
> show #!60 models
> hide #!60 models
> show #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class001.mrc
Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class002.mrc
Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class003.mrc
Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
1.9, shown at level 0.0198, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class004.mrc
Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
1.9, shown at level 0.0163, step 2, values float32
> volume all step 1
> hide #!66 models
> hide #!65 models
> hide #!64 models
> volume #63 level 0.013
> volume #64 level 0.013
> volume #63 level 0.012
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class001.mrc
Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
1.9, shown at level 0.0187, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class002.mrc
Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class003.mrc
Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> volume all step 1
> hide #!68 models
> hide #!69 models
> show #!68 models
> hide #!67 models
> show #!69 models
> hide #!68 models
> volume #69 level 0.013
> volume #68 level 0.013
> volume #67 level 0.013
> show #!67 models
> hide #!67 models
> show #!68 models
> hide #!68 models
> show #!69 models
> hide #!69 models
> show #!29 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> show #!29 models
> hide #!29 models
> hide #!31 models
> show #!28 models
> show #!29 models
> hide #!29 models
> hide #!28 models
> show #!50 models
> hide #!50 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!50 models
> show #!51 models
> hide #!50 models
> hide #!51 models
> show #!53 models
> hide #!53 models
> show #!54 models
> show #!55 models
> hide #!55 models
> hide #!54 models
> show #!50 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> hide #!50 models
> show #!56 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class001.mrc
Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class002.mrc
Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class003.mrc
Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class004.mrc
Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class005.mrc
Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
1.9, shown at level 0.0165, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class006.mrc
Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> hide #!56 models
> volume all step 1
> hide #!71 models
> hide #!72 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> volume #70 level 0.013
> volume #71 level 0.013
> volume #71 level 0.01
> volume #71 level 0.012
> volume #72 level 0.013
> volume #72 level 0.01
> volume #72 level 0.012
> volume #73 level 0.012
> volume #74 level 0.013
> volume #75 level 0.013
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class001.mrc
Opened Cl3D_j577_run_it025_class001.mrc as #76, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class002.mrc
Opened Cl3D_j577_run_it025_class002.mrc as #77, grid size 294,294,294, pixel
1.9, shown at level 0.0135, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class003.mrc
Opened Cl3D_j577_run_it025_class003.mrc as #78, grid size 294,294,294, pixel
1.9, shown at level 0.0153, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class004.mrc
Opened Cl3D_j577_run_it025_class004.mrc as #79, grid size 294,294,294, pixel
1.9, shown at level 0.015, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class005.mrc
Opened Cl3D_j577_run_it025_class005.mrc as #80, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class006.mrc
Opened Cl3D_j577_run_it025_class006.mrc as #81, grid size 294,294,294, pixel
1.9, shown at level 0.0136, step 2, values float32
> volume all step 1
> hide #!77 models
> hide #!78 models
> hide #!79 models
> hide #!80 models
> hide #!81 models
> volume #76 level 0.013
> volume #77 level 0.013
> volume #78 level 0.013
> volume #79 level 0.013
> volume #80 level 0.007565
> volume #80 level 0.02
> volume #80 level 0.012
> volume #81 level 0.012
> volume #81 level 0.01
> volume #81 level 0.008841
> volume #81 level 0.012
> volume #81 level 0.01
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!79 models
> hide #!79 models
> show #!78 models
> hide #!81 models
> hide #!78 models
> show #!77 models
> hide #!77 models
> show #!76 models
> hide #!76 models
> show #!81 models
> hide #!81 models
> show #!80 models
> hide #!80 models
> show #!79 models
> hide #!79 models
> show #!78 models
> hide #!78 models
> show #!77 models
> hide #!77 models
> show #!77 models
> hide #!77 models
> show #!76 models
> hide #!76 models
> show #!76 models
> hide #!76 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> show #!75 models
> hide #!75 models
> show #!74 models
> volume #74 level 0.01584
> volume #74 level 0.01357
> hide #!74 models
> show #!73 models
> hide #!73 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J577_class_02_00082_volume.mrc
Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
128,128,128, pixel 4.36, shown at level 0.888, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J583_class_02_00082_volume.mrc
Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
128,128,128, pixel 4.36, shown at level 0.827, step 1, values float32
> hide #!83 models
> volume #82 level 1.108
> volume #82 level 1.632
> volume #83 level 1.361
> open /Users/cvetkom/Downloads/cryosparc_P17_J610_002_volume_map.mrc
Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
pixel 1.9, shown at level 0.289, step 2, values float32
> volume #84 step 1
> volume #84 level 0.3974
> volume #84 level 0.3145
> volume #84 level 0.3879
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class001.mrc
Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class002.mrc
Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class003.mrc
Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class004.mrc
Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
1.9, shown at level 0.0143, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class005.mrc
Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class006.mrc
Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
1.9, shown at level 0.0179, step 2, values float32
> hide #!84 models
> volume all step 1
> hide #!86 models
> hide #!87 models
> hide #!88 models
> hide #!89 models
> hide #!90 models
> volume #85 level 0.013
> volume #86 level 0.013
> volume #86 level 0.012
> volume #87 level 0.012
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> volume #88 level 0.013
> volume #88 level 0.012
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> hide #!88 models
> show #!89 models
> show #!88 models
> hide #!88 models
> volume #89 level 0.013
> volume #90 level 0.013
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!89 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!84 models
> hide #!84 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class001.mrc
Opened Cl3D_j575_run_it025_class001.mrc as #91, grid size 294,294,294, pixel
1.9, shown at level 0.0167, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class002.mrc
Opened Cl3D_j575_run_it025_class002.mrc as #92, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class003.mrc
Opened Cl3D_j575_run_it025_class003.mrc as #93, grid size 294,294,294, pixel
1.9, shown at level 0.014, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class004.mrc
Opened Cl3D_j575_run_it025_class004.mrc as #94, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class005.mrc
Opened Cl3D_j575_run_it025_class005.mrc as #95, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class006.mrc
Opened Cl3D_j575_run_it025_class006.mrc as #96, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> hide #!92 models
> hide #!93 models
> hide #!94 models
> hide #!95 models
> hide #!96 models
> volume all step 1
> volume #91 level 0.013
> volume #92 level 0.012
> volume #93 level 0.012
> volume #94 level 0.013
> volume #95 level 0.013
> close #91-96
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!88 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!88 models
> hide #!88 models
> show #!88 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> hide #!88 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!70 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!74 models
> hide #!74 models
> show #!73 models
> hide #!73 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!69 models
> hide #!69 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!32 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> hide #!41 models
> hide #!38 models
> show #!82 models
> show #!83 models
> hide #!83 models
> hide #!82 models
> show #!84 models
> hide #!84 models
> show #!82 models
> hide #!82 models
> show #!83 models
> hide #!83 models
> show #!84 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J611_002_volume_map.mrc
Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
pixel 1.9, shown at level 0.273, step 2, values float32
> hide #!84 models
> show #!84 models
> hide #!84 models
> volume #91 step 1
> show #!84 models
> volume #84 level 0.4
> volume #84 level 0.36
> hide #!91 models
> volume #91 level 0.36
> hide #!84 models
> show #!84 models
> hide #!84 models
> volume #91 level 0.4
> volume #91 level 0.45
> show #!84 models
> volume #84 level 0.45
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> show #!84 models
> hide #!84 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!90 models
> hide #!90 models
> show #!85 models
> show #!86 models
> hide #!86 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> hide #!86 models
> show #!28 models
> hide #!28 models
> show #!29 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #!29 models
> show #!29 models
> show #!28 models
> hide #!28 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> show #!28 models
> hide #!28 models
> hide #!31 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!28 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!28 models
> hide #!34 models
> show #!28 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!28 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!32 models
> show #!31 models
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!33 models
> hide #!34 models
> show #!35 models
> show #!32 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!36 models
> show #!37 models
> hide #!36 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!37 models
> show #!37 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!38 models
> hide #!37 models
> show #!39 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!41 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!41 models
> show #!43 models
> hide #!42 models
> hide #!43 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!44 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> hide #!48 models
> show #!49 models
> hide #!49 models
> show #!50 models
> show #!51 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!59 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> hide #!59 models
> show #!63 models
> show #!64 models
> show #!65 models
> hide #!65 models
> show #!66 models
> hide #!64 models
> hide #!63 models
> hide #!66 models
> show #!63 models
> show #!64 models
> hide #!63 models
> hide #!64 models
> show #!67 models
> hide #!67 models
> show #!68 models
> show #!69 models
> hide #!68 models
> show #!68 models
> hide #!69 models
> show #!69 models
> hide #!68 models
> hide #!69 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> hide #!70 models
> show #!75 models
> show #!74 models
> show #!73 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> show #!72 models
> hide #!72 models
> show #!71 models
> hide #!71 models
> show #!70 models
> show #!71 models
> hide #!71 models
> hide #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> show #!75 models
> hide #!74 models
> show #!74 models
> show #!73 models
> hide #!73 models
> hide #!74 models
> hide #!75 models
> show #!76 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> hide #!76 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!85 models
> hide #!85 models
> show #!84 models
> hide #!84 models
> hide #!89 models
> show #!33 models
> show #!32 models
> hide #!32 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> hide #!38 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!70 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!76 models
> show #!75 models
> hide #!75 models
> show #!77 models
> hide #!77 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> hide #!76 models
> show #!85 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!89 models
> hide #!89 models
> show #!89 models
> show #!90 models
> hide #!90 models
> show #!32 models
> show #!34 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!15 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!15 models
> show #!50 models
> show #!51 models
> show #!52 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> hide #!50 models
> hide #!52 models
> show #!51 models
> hide #!51 models
> show #!50 models
> hide #!50 models
> show #!53 models
> hide #!53 models
> show #!54 models
> hide #!54 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> show #!50 models
> hide #!50 models
> show #!51 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!51 models
> show #!51 models
> hide #!57 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!51 models
> show #!51 models
> hide #!51 models
> show #!51 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> show #!55 models
> hide #!55 models
> hide #!51 models
> show #!50 models
> show #!52 models
> hide #!52 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> show #!51 models
> hide #!50 models
> hide #!51 models
> show #!52 models
> hide #!52 models
> show #!53 models
> hide #!53 models
> show #!54 models
> show #!50 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!57 models
> hide #!57 models
> show #!56 models
> hide #!56 models
> show #!56 models
> volume #56 level 0.013
> volume #56 level 0.012
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!56 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!56 models
> hide #!56 models
> show #!59 models
> hide #!59 models
> show #!56 models
> show #!50 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!50 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!58 models
> hide #!58 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!59 models
> show #!60 models
> hide #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> show #!57 models
> hide #!57 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> show #!60 models
> hide #!59 models
> show #!59 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!56 models
> hide #!59 models
> show #!63 models
> hide #!63 models
> show #!2 models
> hide #!2 models
> show #!63 models
> show #!64 models
> hide #!63 models
> show #!65 models
> hide #!65 models
> show #!66 models
> hide #!64 models
> hide #!66 models
> show #!67 models
> hide #!67 models
> show #!68 models
> show #!69 models
> hide #!68 models
> hide #!69 models
> show #!70 models
> hide #!70 models
> show #!69 models
> hide #!69 models
> show #!68 models
> hide #!68 models
> show #!69 models
> show #!68 models
> hide #!68 models
> hide #!69 models
> show #!67 models
> show #!68 models
> hide #!67 models
> show #!69 models
> hide #!69 models
> show #!69 models
> hide #!68 models
> show #!59 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!69 models
> show #!69 models
> hide #!69 models
> show #!69 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> hide #!69 models
> show #!63 models
> show #!64 models
> hide #!63 models
> hide #!64 models
> show #!28 models
> show #!29 models
> hide #!28 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!29 models
> hide #!31 models
> show #!32 models
> show #!33 models
> show #!34 models
> show #!35 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!32 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!28 models
> hide #!28 models
> show #!29 models
> hide #!29 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!32 models
> show #!34 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!37 models
> show #!38 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #!37 models
> show #!38 models
> hide #!38 models
> show #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> hide #!36 models
> show #!36 models
> hide #!38 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!38 models
> hide #!32 models
> show #!39 models
> hide #!39 models
> show #!40 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> show #!42 models
> hide #!41 models
> show #!43 models
> hide #!42 models
> show #!42 models
> hide #!43 models
> show #!41 models
> hide #!42 models
> hide #!41 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!44 models
> show #!45 models
> hide #!44 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> show #!49 models
> hide #!48 models
> hide #!49 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!44 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!48 models
> show #!49 models
> hide #!48 models
> hide #!49 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!44 models
> hide #!44 models
> show #!45 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!37 models
> hide #!37 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> show #!70 models
> show #!71 models
> hide #!70 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!75 models
> show #!70 models
> hide #!70 models
> show #!71 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!74 models
> show #!72 models
> hide #!72 models
> show #!71 models
> show #!73 models
> hide #!73 models
> hide #!71 models
> show #!71 models
> hide #!71 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> hide #!74 models
> hide #!70 models
> show #!76 models
> hide #!76 models
> show #!75 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!75 models
> show #!76 models
> show #!77 models
> hide #!76 models
> show #!78 models
> hide #!78 models
> show #!79 models
> hide #!79 models
> show #!80 models
> hide #!80 models
> show #!81 models
> hide #!81 models
> close #76-81
> show #!85 models
> show #!86 models
> hide #!86 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!85 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!86 models
> hide #!87 models
> show #!88 models
> show #!89 models
> show #!85 models
> hide #!85 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> hide #!85 models
> show #!85 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!89 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!89 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!90 models
> hide #!89 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!88 models
> hide #!88 models
> show #!87 models
> hide #!87 models
> show #!86 models
> hide #!86 models
> show #!56 models
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!57 models
> show #!58 models
> hide #!58 models
> show #!59 models
> hide #!56 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!56 models
> show #!59 models
> hide #!59 models
> hide #!56 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 models
> show #!35 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> hide #!35 models
> show #!85 models
> show #!86 models
> hide #!86 models
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> hide #!85 models
> show #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> hide #!87 models
> show #!89 models
> hide #!89 models
> show #!90 models
> hide #!90 models
> show #!85 models
> hide #!85 models
> show #!86 models
> show #!87 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> hide #!87 models
> hide #!86 models
> show #!86 models
> hide #!86 models
> show #!86 models
> show #!87 models
> hide #!86 models
> show #!86 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> show #!87 models
> show #!89 models
> hide #!89 models
> show #!89 models
> hide #!89 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!86 models
> show #!86 models
> show #!87 models
> hide #!87 models
> show #!87 models
> hide #!87 models
> hide #!86 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> hide #!40 models
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!42 models
> hide #!42 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!39 models
> show #!40 models
> hide #!40 models
> hide #!39 models
> show #!41 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!43 models
> show #!41 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> hide #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> show #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> hide #!43 models
> show #!41 models
> show #!42 models
> hide #!41 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!41 models
> show #!42 models
> show #!43 models
> hide #!43 models
> hide #!42 models
> hide #!41 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!35 models
> show #!34 models
> hide #!35 models
> show #!35 models
> hide #!34 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!34 models
> hide #!34 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!91 models
> hide #!91 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J615_class_00_final_volume.mrc
Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J616_class_00_final_volume.mrc
Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
192,192,192, pixel 2.91, shown at level 0.499, step 1, values float32
> volume #76 level 0.4164
> volume #77 level 0.4158
> volume #76 level 0.4
> volume #76 level 0.3
> volume #76 level 0.35
> volume #76 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J621_mask.mrc
Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #78 level 1
> volume #78 color #cccc9980
> open /Users/cvetkom/Downloads/cryosparc_P17_J617_class_00_final_volume.mrc
Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
192,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
> hide #!78 models
> hide #!79 models
> show #!79 models
> hide #!79 models
> show #!79 models
> hide #!76 models
> volume #79 level 0.3
> volume #79 level 0.4
> volume #79 level 0.35
> volume #79 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
pixel 1.9, shown at level 0.339, step 2, values float32
> hide #!79 models
> volume #80 step 1
> volume #80 level 0.3095
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> hide #!81 models
> show #!81 models
> hide #!80 models
> volume #81 step 1
> show #!80 models
> hide #!80 models
> volume #81 level 0.35
> hide #!81 models
> show #!80 models
> volume #80 level 0.35
> volume #80 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J619_class_00_final_volume.mrc
Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
192,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
> hide #!80 models
> show #!79 models
> hide #!79 models
> volume #92 level 0.35
> volume #92 level 0.4
> volume #92 level 0.4136
> show #!79 models
> hide #!92 models
> volume #79 level 0.3729
> show #!76 models
> hide #!79 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J623_007_volume_map.mrc
Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
pixel 1.9, shown at level 0.341, step 2, values float32
> hide #!76 models
> volume #93 step 1
> volume #93 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J626_class_01_00400_volume.mrc
Opened cryosparc_P17_J626_class_01_00400_volume.mrc as #94, grid size
128,128,128, pixel 4.36, shown at level 1.11, step 1, values float32
> hide #!93 models
> volume #94 level 0.8311
> close #94
> open /Users/cvetkom/Downloads/cryosparc_P17_J625_007_volume_map.mrc
Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
pixel 1.9, shown at level 0.341, step 2, values float32
> volume #94 step 1
> volume #94 level 0.3
> volume #94 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J631_class_01_00042_volume.mrc
Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J629_class_01_00042_volume.mrc
Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J628_class_01_00042_volume.mrc
Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
128,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
> hide #!94 models
> hide #!95 models
> hide #!96 models
> volume #97 level 1.082
> volume #97 level 1
> volume #96 level 1
> volume #95 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
Opened cryosparc_P17_J620_007_volume_map.mrc as #98, grid size 294,294,294,
pixel 1.9, shown at level 0.339, step 2, values float32
> close #98
> show #!80 models
> show #!93 models
Drag select of 80 cryosparc_P17_J620_007_volume_map.mrc , 93
cryosparc_P17_J623_007_volume_map.mrc
> select clear
> hide #!93 models
> show #!93 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> lighting soft
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!82 models
> hide #!82 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> show #!80 models
> hide #!80 models
> hide #!93 models
> show #!81 models
> show #!80 models
> hide #!80 models
> volume #81 level 0.32
> volume #81 level 0.35
> show #!80 models
> select add #81
2 models selected
> ui mousemode right "rotate selected models"
> select subtract #81
Nothing selected
> hide #!81 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class006.mrc
Opened run_it025_class006.mrc as #98, grid size 294,294,294, pixel 1.9, shown
at level 0.0154, step 2, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class003.mrc
Opened run_it025_class003.mrc as #99, grid size 294,294,294, pixel 1.9, shown
at level 0.0157, step 2, values float32
> hide #!80 models
> hide #!98 models
> hide #!99 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class001.mrc
Opened run_it025_class001.mrc as #100, grid size 294,294,294, pixel 1.9, shown
at level 0.0158, step 2, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class002.mrc
Opened run_it025_class002.mrc as #101, grid size 294,294,294, pixel 1.9, shown
at level 0.0166, step 2, values float32
> hide #!101 models
> volume #98 step 1
> volume #99 step 1
> volume #100 step 1
> volume #101 step 1
> volume #100 level 0.01165
> volume #101 level 0.01425
> volume #101 level 0.01268
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!100 models
> show #!32 models
> volume #100 level 0.02
> hide #!32 models
> show #!32 models
> volume #100 level 0.015
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> volume #100 level 0.014
> volume #100 level 0.013
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> volume #101 level 0.014
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #!101 models
> show #!99 models
> show #!98 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!85 models
> hide #!85 models
> show #!88 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!88 models
> hide #!88 models
> show #!39 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!40 models
> show #!40 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> hide #!40 models
> close #98-101
> show #!97 models
> hide #!97 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
1.9, shown at level 0.018, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class001.mrc
Opened Cl3D_j585_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class002.mrc
Opened Cl3D_j585_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class003.mrc
Opened Cl3D_j585_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class004.mrc
Opened Cl3D_j585_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class005.mrc
Opened Cl3D_j585_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.016, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class006.mrc
Opened Cl3D_j585_run_it025_class006.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.0002, step 2, values float32
> volume all step 1
> hide #!99 models
> hide #!100 models
> hide #!101 models
> hide #!102 models
> hide #!103 models
> hide #!104 models
> hide #!105 models
> hide #!106 models
> hide #!107 models
> hide #!108 models
> hide #!109 models
> hide #!110 models
> volume #98 level 0.013
> volume #98 level 0.012
> volume #99 level 0.012
> volume #100 level 0.013
> volume #101 level 0.012
> volume #102 level 0.012
> volume #103 level 0.013
> ui mousemode right zoom
> lighting simple
> show #!98 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> hide #!103 models
> show #!104 models
> show #!103 models
> hide #!104 models
> show #!104 models
> volume #104 level 0.013
> show #!103 models
> hide #!103 models
> volume #105 level 0.013
> volume #106 level 0.013
> volume #106 level 0.012
> volume #105 level 0.012
> volume #107 level 0.013
> volume #108 level 0.013
> volume #109 level 0.013
> volume #110 level -0.02134
> close #110
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class001.mrc
Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class002.mrc
Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
1.9, shown at level 0.017, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class003.mrc
Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class004.mrc
Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class005.mrc
Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
1.9, shown at level 0.0127, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class006.mrc
Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class007.mrc
Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
1.9, shown at level 0.0179, step 2, values float32
> close #105-109
> hide #!111 models
> hide #!112 models
> hide #!113 models
> hide #!114 models
> hide #!115 models
> hide #!116 models
> volume #110 level 0.012
> volume #111 level 0.012
> volume #111 level 0.013
> volume #110 step 1
> volume #111 step 1
> volume #112 step 1
> volume #112 level 0.013
> volume #113 step 1
> volume #113 level 0.012
> volume #114 step 1
> volume #114 level 0.012
> volume #115 step 1
> volume #115 level 0.013
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> show #!112 models
> hide #!112 models
> volume #116 step 1
> volume #116 level 0.013
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> volume #111 level 0.01556
> volume #111 level 0.01455
> show #!110 models
> hide #!110 models
> hide #!111 models
> show #!111 models
> show #!99 models
> hide #!111 models
> show #!98 models
> hide #!99 models
> show #!110 models
> hide #!110 models
> hide #!98 models
> show #!110 models
> hide #!110 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class001.mrc
Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class002.mrc
Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class003.mrc
Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
1.9, shown at level 0.0195, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class004.mrc
Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class005.mrc
Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class001.mrc
Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class002.mrc
Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class003.mrc
Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
1.9, shown at level 0.0197, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class004.mrc
Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class005.mrc
Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
1.9, shown at level 0.0161, step 2, values float32
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
\u2014\u2014\u2014 End of log from Mon Jun 3 09:50:12 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!105 models
> show #!105 models
> show #!111 models
> hide #!111 models
> hide #!105 models
> show #!105 models
> hide #!105 models
> show #!105 models
> volume #105,106,107,108,109,117,118,119,120,121 level 0.013
> hide #!106 models
> show #!106 models
> hide #!109 models
> hide #!121 models
> hide #!120 models
> hide #!119 models
> hide #!118 models
> hide #!117 models
> hide #!108 models
> hide #!107 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!105 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!107 models
> hide #!107 models
> show #!108 models
> hide #!108 models
> show #!109 models
> hide #!109 models
> show #!108 models
> show #!109 models
> hide #!109 models
> show #!109 models
> hide #!109 models
> hide #!108 models
> show #!121 models
> hide #!121 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job325_0p95apix.mrc
Opened Ref3D_job325_0p95apix.mrc as #122, grid size 588,588,588, pixel 0.95,
shown at level 0.0107, step 4, values float32
> close #122
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> show #!2 models
> volume #2 level 0.003218
> volume #2 level 0.006199
> volume #2 level 0.013
> hide #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
\u2014\u2014\u2014 End of log from Tue Jun 11 16:35:40 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!119 models
> hide #!119 models
> show #!120 models
> hide #!120 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class001.mrc
Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
1.9, shown at level 0.0174, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class002.mrc
Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class003.mrc
Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
1.9, shown at level 0.0127, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class004.mrc
Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
1.9, shown at level 0.0134, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class005.mrc
Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class006.mrc
Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
1.9, shown at level 0.0155, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class007.mrc
Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
1.9, shown at level 0.0175, step 2, values float32
> volume all step 1
> hide #!123 models
> hide #!124 models
> hide #!125 models
> hide #!126 models
> hide #!127 models
> hide #!128 models
> volume #122 level 0.01525
> volume #122 level 0.013
> volume #123 level 0.013
> show #!74 models
> volume #122 level 0.014
> volume #122 level 0.015
> hide #!74 models
> volume #124 level 0.013
> volume #125 level 0.013
> volume #126 level 0.013
> volume #127 level 0.013
> volume #128 level 0.014
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/run_it025_class001.mrc
Opened run_it025_class001.mrc as #129, grid size 294,294,294, pixel 1.9, shown
at level 0.0173, step 2, values float32
> close #129
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class001.mrc
Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
1.9, shown at level 0.0173, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class002.mrc
Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
1.9, shown at level 0.0159, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class003.mrc
Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class004.mrc
Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
1.9, shown at level 0.0132, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class005.mrc
Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class006.mrc
Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
1.9, shown at level 0.0156, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class007.mrc
Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
1.9, shown at level 0.0169, step 2, values float32
> volume all step 1
> hide #!130 models
> hide #!131 models
> hide #!132 models
> hide #!133 models
> hide #!134 models
> hide #!135 models
> volume #129 level 0.015
> volume #129 level 0.014
> show #!130 models
> hide #!129 models
> volume #130 level 0.013
> volume #132 level 0.013
> volume #133 level 0.013
> volume #134 level 0.014
> volume #134 level 0.013
> volume #135 level 0.014
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> show #!133 models
> hide #!133 models
> hide #!135 models
> show #!134 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!135 models
> hide #!135 models
> show #!134 models
> hide #!134 models
> show #!133 models
> hide #!133 models
> show #!134 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!130 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class001.mrc
Opened Cl3D_j619_run_it025_class001.mrc as #136, grid size 320,320,320, pixel
1.9, shown at level 0.0108, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class002.mrc
Opened Cl3D_j619_run_it025_class002.mrc as #137, grid size 320,320,320, pixel
1.9, shown at level 0.00682, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class003.mrc
Opened Cl3D_j619_run_it025_class003.mrc as #138, grid size 320,320,320, pixel
1.9, shown at level 0.0091, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class004.mrc
Opened Cl3D_j619_run_it025_class004.mrc as #139, grid size 320,320,320, pixel
1.9, shown at level 0.0104, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class005.mrc
Opened Cl3D_j619_run_it025_class005.mrc as #140, grid size 320,320,320, pixel
1.9, shown at level 0.0128, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class006.mrc
Opened Cl3D_j619_run_it025_class006.mrc as #141, grid size 320,320,320, pixel
1.9, shown at level 0.013, step 2, values float32
> volume all step 1
> hide #!137 models
> hide #!138 models
> hide #!139 models
> hide #!140 models
> hide #!141 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!137 models
> hide #!137 models
> show #!136 models
> hide #!136 models
> show #!136 models
> hide #!136 models
> show #!137 models
> show #!138 models
> hide #!138 models
> show #!138 models
> hide #!137 models
> hide #!138 models
> show #!139 models
> hide #!139 models
> show #!140 models
> show #!141 models
> hide #!140 models
> hide #!141 models
> close #136-141
> show #!130 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> hide #!130 models
> show #!117 models
> show #!118 models
> hide #!118 models
> show #!118 models
> hide #!118 models
> show #!118 models
> hide #!117 models
> show #!117 models
> hide #!118 models
> show #!118 models
> hide #!117 models
> hide #!118 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> hide #!110 models
> show #!105 models
> show #!106 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> show #!106 models
> hide #!106 models
> hide #!105 models
> show #!105 models
> show #!106 models
> hide #!105 models
> hide #!106 models
> show #!110 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> show #!122 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!110 models
> show #!99 models
> hide #!99 models
> show #!98 models
> volume #98 level 0.013
> hide #!130 models
> show #!130 models
> volume #99 level 0.013
> hide #!130 models
> show #!110 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> volume #110 level 0.013
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> hide #!110 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!129 models
> hide #!129 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J680_volume_map.mrc
Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
1.9, shown at level 0.413, step 2, values float32
> hide #!130 models
> volume #136 step 1
> volume #136 level 0.314
> open /Users/cvetkom/Downloads/cryosparc_P17_J676_class_00_final_volume.mrc
Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
192,192,192, pixel 2.91, shown at level 0.536, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J678_class_00_final_volume.mrc
Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
192,192,192, pixel 2.91, shown at level 0.529, step 1, values float32
> hide #!136 models
> hide #!138 models
> volume #137 level 0.5
> volume #137 level 0.4
> volume #137 level 0.3
> volume #138 level 0.3
> hide #!138 models
> show #!137 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J681_volume_map.mrc
Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
1.9, shown at level 0.411, step 2, values float32
> hide #!137 models
> volume #139 step 1
> volume #139 level 0.2939
> open /Users/cvetkom/Downloads/cryosparc_P17_J684_010_volume_map.mrc
Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J685_007_volume_map.mrc
Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
pixel 1.9, shown at level 0.361, step 2, values float32
> hide #!139 models
> hide #!141 models
> volume #140 step 1
> volume #141 step 1
> volume #141 level 0.35
> volume #140 level 0.36
> volume #141 level 0.36
> open /Users/cvetkom/Downloads/cryosparc_P17_J677_class_00_final_volume.mrc
Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
192,192,192, pixel 2.91, shown at level 0.561, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J679_class_00_final_volume.mrc
Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
192,192,192, pixel 2.91, shown at level 0.55, step 1, values float32
> hide #!141 models
> hide #!143 models
> volume #142 level 0.3
> hide #!142 models
> show #!143 models
> volume #143 level 0.3
> volume #143 level 0.25
> volume #142 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J686_mask.mrc
Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #144 level 1
> transparency #142.1#144.1 50
> transparency #142.1#144.1 0
> volume #144 color #cccc9980
> volume #142 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J688_007_volume_map.mrc
Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J689_008_volume_map.mrc
Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> hide #!142 models
> hide #!144 models
> hide #!146 models
> volume #145 step 1
> show #!146 models
> hide #!145 models
> volume #146 step 1
> show #!145 models
> hide #!145 models
> show #!145 models
> hide #!146 models
> show #!146 models
> hide #!145 models
> show #!145 models
> hide #!146 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J690_006_volume_map.mrc
Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!145 models
> volume #147 step 1
> lighting soft
> show #!145 models
> hide #!147 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J691_008_volume_map.mrc
Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
pixel 1.9, shown at level 0.365, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J692_009_volume_map.mrc
Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
pixel 1.9, shown at level 0.366, step 2, values float32
> hide #!145 models
> hide #!149 models
> volume #148 step 1
> volume #149 step 1
> lighting soft
> lighting simple
> lighting soft
> show #!145 models
> hide #!149 models
> show #!146 models
> hide #!145 models
> hide #!146 models
> show #!145 models
> show #!148 models
> hide #!148 models
> show #!148 models
> show #!149 models
> hide #!149 models
> hide #!148 models
> show #!147 models
> hide #!147 models
> hide #!145 models
> show #!147 models
> hide #!147 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_map.mrc
Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> volume #150 step 1
> show #!149 models
> hide #!149 models
> show #!149 models
> hide #!149 models
> show #!145 models
> hide #!150 models
> hide #!145 models
> show #!146 models
> hide #!146 models
> volume flip #145,146,148,149
Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> hide #!154 models
> hide #!153 models
> hide #!152 models
> show #!150 models
> show #!152 models
> show #!153 models
> show #!154 models
> select add #150
2 models selected
> select add #151
4 models selected
> select add #152
6 models selected
> select add #153
8 models selected
> select add #154
10 models selected
> lighting simple
> select subtract #150
8 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #151,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#152,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#153,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#154,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87
> view matrix models
> #151,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#152,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#153,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#154,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38
> view matrix models
> #151,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#152,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#153,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#154,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58
> view matrix models
> #151,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#152,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#153,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#154,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2
> ui mousemode right "translate selected models"
> view matrix models
> #151,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#152,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#153,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#154,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84
> ui mousemode right "rotate selected models"
> view matrix models
> #151,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#152,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#153,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#154,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57
> ui mousemode right "translate selected models"
> view matrix models
> #151,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#152,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#153,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#154,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75
> select subtract #151
6 models selected
> select subtract #152
4 models selected
> select add #152
6 models selected
> select add #151
8 models selected
> select subtract #151
6 models selected
> select subtract #152
4 models selected
> select subtract #153
2 models selected
> select subtract #154
Nothing selected
> ui tool show "Fit in Map"
> fitmap #151 inMap #150
Fit map cryosparc_P17_J688_007_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 254273 points
correlation = 0.995, correlation about mean = 0.9397, overlap = 9.223e+04
steps = 100, shift = 5.99, angle = 2.29 degrees
Position of cryosparc_P17_J688_007_volume_map.mrc z flip (#151) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999140 -0.00359338 0.00207026 559.46992299
-0.00342330 0.99702499 0.07700290 -19.07074818
-0.00234080 0.07699515 -0.99702872 534.50211369
Axis -0.00175550 0.99925597 0.03852822
Axis point 280.01335285 0.00000000 267.30976851
Rotation angle (degrees) 179.87353804
Shift along axis 0.55470700
> fitmap #152 inMap #150
Fit map cryosparc_P17_J689_008_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 253853 points
correlation = 0.995, correlation about mean = 0.939, overlap = 9.217e+04
steps = 80, shift = 5.92, angle = 2.24 degrees
Position of cryosparc_P17_J689_008_volume_map.mrc z flip (#152) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999493 -0.00290598 0.00130357 559.46976174
-0.00279515 0.99693412 0.07819562 -19.59657377
-0.00152681 0.07819157 -0.99693718 533.82278737
Axis -0.00142641 0.99923323 0.03912681
Axis point 279.91004169 0.00000000 267.09682063
Rotation angle (degrees) 179.91885345
Shift along axis 0.50720275
> fitmap #153 inMap #150
Fit map cryosparc_P17_J691_008_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 254067 points
correlation = 0.9949, correlation about mean = 0.9379, overlap = 9.218e+04
steps = 100, shift = 5.99, angle = 2.29 degrees
Position of cryosparc_P17_J691_008_volume_map.mrc z flip (#153) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999153 -0.00354328 0.00209321 559.43919323
-0.00337135 0.99701735 0.07710412 -19.11074723
-0.00236017 0.07709641 -0.99702085 534.50415261
Axis -0.00172997 0.99925406 0.03857895
Axis point 280.00103027 0.00000000 267.30909738
Rotation angle (degrees) 179.87232473
Shift along axis 0.55630498
> fitmap #154 inMap #150
Fit map cryosparc_P17_J692_009_volume_map.mrc z flip in map
cryosparc_P17_J693_006_volume_map.mrc using 253930 points
correlation = 0.9949, correlation about mean = 0.9381, overlap = 9.218e+04
steps = 76, shift = 5.97, angle = 2.31 degrees
Position of cryosparc_P17_J692_009_volume_map.mrc z flip (#154) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
-0.99999289 -0.00347463 0.00146599 559.52836319
-0.00335259 0.99707669 0.07633372 -18.91952628
-0.00172694 0.07632826 -0.99708125 534.48491699
Axis -0.00170809 0.99926890 0.03819344
Axis point 279.96163715 0.00000000 267.38037953
Rotation angle (degrees) 179.90846237
Shift along axis 0.55239822
> hide #!152 models
> hide #!153 models
> hide #!154 models
> volume #151 level 0.37
> ui mousemode right zoom
> lighting soft
> hide #!153 models
> show #!153 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!154 models
> hide #!154 models
> show #!153 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!150 models
> hide #!154 models
> show #!32 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> hide #!32 models
> show #!32 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!32 models
> show #!32 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!32 models
> show #!130 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J699_class_00_00042_volume.mrc
Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
128,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
> hide #!75 models
> hide #!130 models
> volume #155 level 1.1
> volume #155 level 0.5
> volume #155 level 0.6
> volume #155 level 0.55
> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask.mrc
Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #156 level 1
> volume #156 color #ffffb27e
> volume #156 color #ffffb27d
> open /Users/cvetkom/Downloads/cryosparc_P17_J697_006_volume_map.mrc
Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> hide #!155 models
> hide #!156 models
> volume #157 step 1
> volume #157 level 0.3
> volume #157 level 0.32
> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask(1).mrc
Opened cryosparc_P17_J700_mask(1).mrc as #158, grid size 128,128,128, pixel
4.36, shown at level 1, step 1, values float32
> hide #!157 models
> show #!155 models
> show #!156 models
> hide #!156 models
> volume #158 color #b2b2ff7e
> volume #158 color #b2b2ff7d
> volume #158 level 1
> volume #155 level 0.8
> open /Users/cvetkom/Downloads/cryosparc_P17_J701_006_volume_map.mrc
Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J703_007_volume_map.mrc
Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!155 models
> hide #!158 models
> volume #159 step 1
> volume #160 step 1
> show #!159 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!157 models
> hide #!159 models
> show #!149 models
> hide #!149 models
> show #!149 models
> hide #!149 models
> show #!159 models
> show #!160 models
> select add #159
2 models selected
> select add #160
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #159,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73,#160,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73
> view matrix models
> #159,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69,#160,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69
> select subtract #159
2 models selected
> select subtract #160
Nothing selected
> hide #!159 models
> hide #!160 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!154 models
> hide #!154 models
> show #!159 models
> hide #!159 models
> hide #!157 models
> show #!159 models
> show #!160 models
> hide #!159 models
> hide #!160 models
> show #!157 models
> volume #157 level 0.36
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!157 models
> volume flip #157
Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> hide #!159 models
> show #!159 models
> hide #!161 models
> show #!161 models
> select add #161
2 models selected
> view matrix models
> #161,0.76891,-0.22832,0.5972,-18.442,0.24486,-0.75768,-0.60494,582.05,0.59061,0.61138,-0.52668,39.302
> view matrix models
> #161,0.67534,0.22196,0.70331,-146.74,0.10898,-0.9732,0.20249,480.95,0.72941,-0.060102,-0.68143,229.96
> view matrix models
> #161,-0.93098,0.36002,0.06057,425.2,0.36288,0.89435,0.26166,-136.94,0.040032,0.26557,-0.96326,401.04
> view matrix models
> #161,-0.89701,0.43896,0.051772,395.36,0.44113,0.89642,0.042718,-105.12,-0.027658,0.061157,-0.99774,486.85
> select subtract #161
Nothing selected
> fitmap #161 inMap #159
Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
cryosparc_P17_J701_006_volume_map.mrc using 252025 points
correlation = 0.9982, correlation about mean = 0.9798, overlap = 9.355e+04
steps = 112, shift = 10, angle = 4.47 degrees
Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
cryosparc_P17_J701_006_volume_map.mrc (#159) coordinates:
Matrix rotation and translation
-0.99987255 -0.01520153 -0.00487783 564.75986128
0.01517723 -0.99987242 0.00497921 552.56953504
-0.00495290 0.00490455 0.99997571 0.88182116
Axis -0.00245783 0.00247107 0.99999393
Axis point 280.28257868 278.42842383 0.00000000
Rotation angle (degrees) 179.12967387
Shift along axis 0.85917190
> hide #!161 models
> show #!161 models
> hide #!159 models
> show #!159 models
> hide #!161 models
> show #!161 models
> hide #!159 models
> show #!159 models
> hide #!161 models
> hide #!159 models
> show #!155 models
> hide #!155 models
> show #!151 models
> volume #151 level 0.36
> ui mousemode right zoom
> show #!153 models
> show #!154 models
> hide #!153 models
> hide #!154 models
> hide #!151 models
> show #!151 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!151 models
> show #!150 models
> hide #!150 models
> show #!150 models
> volume #150 level 0.36
> hide #!81 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!81 models
> show #!81 models
> hide #!81 models
> hide #!150 models
> show #!150 models
> show #!157 models
> hide #!157 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> show #!160 models
> select add #159
2 models selected
> select add #160
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #159,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66,#160,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66
> ui mousemode right "rotate selected models"
> view matrix models
> #159,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92,#160,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92
> select subtract #160
2 models selected
> select subtract #159
Nothing selected
> fitmap #159 inMap #150
Fit map cryosparc_P17_J701_006_volume_map.mrc in map
cryosparc_P17_J693_006_volume_map.mrc using 253555 points
correlation = 0.995, correlation about mean = 0.9467, overlap = 9.384e+04
steps = 92, shift = 15.9, angle = 4.91 degrees
Position of cryosparc_P17_J701_006_volume_map.mrc (#159) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
0.99990377 -0.01280700 0.00533263 1.75411257
-0.01349030 -0.98727395 0.15845557 514.15896836
0.00323543 -0.15851226 -0.98735171 596.92132464
Axis -0.99997579 0.00661630 -0.00215569
Axis point 0.00000000 280.88748875 277.95683594
Rotation angle (degrees) 170.88086929
Shift along axis 0.36097960
> fitmap #160 inMap #150
Fit map cryosparc_P17_J703_007_volume_map.mrc in map
cryosparc_P17_J693_006_volume_map.mrc using 254051 points
correlation = 0.9949, correlation about mean = 0.946, overlap = 9.382e+04
steps = 140, shift = 15.9, angle = 4.85 degrees
Position of cryosparc_P17_J703_007_volume_map.mrc (#160) relative to
cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
Matrix rotation and translation
0.99989095 -0.01388197 0.00503895 2.09422029
-0.01450557 -0.98723491 0.15860902 514.34229109
0.00277282 -0.15866482 -0.98732861 597.00803822
Axis -0.99997256 0.00714230 -0.00196544
Axis point 0.00000000 281.00771740 277.97254777
Rotation angle (degrees) 170.87196021
Shift along axis 0.40604025
> hide #!160 models
> hide #!159 models
> show #!159 models
> hide #!150 models
> show #!157 models
> hide #!157 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!160 models
> hide #!160 models
> show #!161 models
> hide #!161 models
> show #!159 models
> show #!161 models
> hide #!161 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!160 models
> hide #!159 models
> show #!159 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!159 models
> hide #!160 models
> show #!160 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> hide #!160 models
> show #!159 models
> hide #!159 models
> show #!157 models
> show #!159 models
> hide #!159 models
> hide #!157 models
> show #!150 models
> show #!159 models
> hide #!159 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> show #!159 models
> hide #!150 models
> show #!150 models
> hide #!159 models
> hide #!150 models
> show #!151 models
> show #!150 models
> hide #!151 models
> show #!151 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> show #!150 models
> hide #!150 models
> hide #!151 models
> show #!150 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_mask_refine.mrc
Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
294,294,294, pixel 1.9, shown at level 1, step 2, values float32
> volume #162 step 1
> volume #162 color #e5bf9980
> volume #162 level 1
> volume #162 color #e5bf9967
> volume #162 color #e5bf9966
> volume #150 level 0.3
> volume #150 level 0.2
> hide #!162 models
> show #!162 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J704_mask.mrc
Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> hide #!162 models
> volume #163 step 1
> volume #163 color #99bfe565
> volume #163 color #99bfe566
> volume #163 level 1
> show #!162 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!163 models
> show #!163 models
> hide #!162 models
> show #!162 models
> hide #!162 models
> show #!162 models
> hide #!162 models
> volume #163 level 0.5
> volume #163 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J707_009_volume_map.mrc
Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> hide #!163 models
> hide #!150 models
> volume #164 step 1
> volume #164 level 0.384
> volume #164 level 0.35
> volume #164 level 0.3
> volume #164 level 0.2
> open /Users/cvetkom/Downloads/cryosparc_P17_J708_mask.mrc
Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> hide #!164 models
> show #!164 models
> hide #!165 models
> show #!165 models
> volume #165 step 1
> volume #165 level 1
> volume #165 color #b2b2b27c
> volume #165 color #b2b2b26b
> volume #165 color #b2b2b263
> volume #165 color #b2b2b265
> volume #165 color #b2b2b266
> hide #!165 models
> volume #164 level 0.5
> volume #164 level 0.4
> open /Users/cvetkom/Downloads/cryosparc_P17_J705_006_volume_map.mrc
Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
pixel 1.9, shown at level 0.359, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J706_004_volume_map.mrc
Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
> hide #!164 models
> volume #166 step 1
> volume #167 step 1
> show #!164 models
> hide #!167 models
> show #!165 models
> hide #!165 models
> hide #!164 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J695_class_00_final_volume.mrc
Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
192,192,192, pixel 2.91, shown at level 0.544, step 1, values float32
> volume #168 level 0.3
> volume #168 level 0.25
> volume #168 level 0.3
> open /Users/cvetkom/Downloads/cryosparc_P17_J714_mask.mrc
Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #169 color #ffb2ff7d
> volume #169 color #ffb2ff67
> volume #169 color #ffb2ff66
> volume #169 level 1
> hide #!168 models
> show #!168 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask.mrc
Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #170 color #ffb2b266
> volume #170 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask(1).mrc
Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
2.91, shown at level 1, step 1, values float32
> volume #171 color #b2ffb266
> volume #171 level 1
> show #!169 models
> hide #!171 models
> show #!171 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!169 models
> hide #!169 models
> show #!170 models
> hide #!171 models
> show #!171 models
> hide #!171 models
> show #!171 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> hide #!168 models
> hide #!170 models
> hide #!171 models
> volume #172 step 1
> show #!168 models
> hide #!168 models
> show #!168 models
> hide #!168 models
> show #!164 models
> hide #!164 models
> show #!164 models
> hide #!172 models
> show #!172 models
> hide #!164 models
> volume #172 level 0.4
> volume #172 level 0.38
> volume #172 level 0.36
> open /Users/cvetkom/Downloads/cryosparc_P17_J710_008_volume_map.mrc
Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J712_007_volume_map.mrc
Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
pixel 1.9, shown at level 0.349, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J711_009_volume_map.mrc
Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
pixel 1.9, shown at level 0.353, step 2, values float32
> hide #!172 models
> hide #!174 models
> hide #!173 models
> show #!173 models
> hide #!175 models
> volume #173 step 1
> volume #174 step 1
> volume #175 step 1
> volume #173 level 0.3
> volume #173 level 0.2
> show #!164 models
> hide #!164 models
> show #!175 models
> volume #175 level 0.2
> hide #!175 models
> show #!175 models
> hide #!173 models
> show #!173 models
> hide #!175 models
> show #!175 models
> hide #!175 models
> volume #173 level 0.25
> volume #173 level 0.2
> volume #173 level 0.25
> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> volume #176 step 1
> volume #176 color #ffffb266
> volume #176 level 1
> close #176
> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
shown at level 1, step 2, values float32
> volume #176 step 1
> volume #176 color #b2ffff66
> volume #176 level 1
> show #!174 models
> hide #!173 models
> hide #!176 models
> volume #174 level 0.2
> volume #174 level 0.25
> volume #174 level 0.2
> show #!173 models
> hide #!174 models
> show #!174 models
> hide #!173 models
> hide #!174 models
> show #!151 models
> show #!152 models
> show #!153 models
> show #!154 models
> hide #!154 models
> hide #!153 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!153 models
> hide #!151 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!153 models
> show #!153 models
> hide #!153 models
> show #!153 models
> hide #!154 models
> show #!152 models
> hide #!152 models
> hide #!153 models
> show #!152 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!152 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!151 models
> show #!151 models
> hide #!152 models
> show #!153 models
> hide #!153 models
> show #!147 models
> hide #!151 models
> hide #!147 models
> show #!147 models
> show #!145 models
> hide #!145 models
> hide #!147 models
> show #!145 models
> hide #!145 models
> show #!175 models
> show #!174 models
> hide #!175 models
> hide #!174 models
> show #!167 models
> hide #!167 models
> show #!168 models
> hide #!168 models
> show #!167 models
> hide #!167 models
> show #!168 models
> hide #!168 models
> show #!166 models
> hide #!166 models
> show #!173 models
> show #!174 models
> hide #!174 models
> hide #!173 models
> show #!161 models
> hide #!161 models
> show #!160 models
> hide #!160 models
> show #!154 models
> show #!153 models
> hide #!154 models
> show #!154 models
> hide #!154 models
> hide #!153 models
> show #!152 models
> show #!153 models
> hide #!153 models
> hide #!152 models
> show #!151 models
> hide #!151 models
> show #!150 models
> hide #!150 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
> ui mousemode right zoom
[Repeated 1 time(s)]
> show #!176 models
> hide #!176 models
> show #!175 models
> hide #!175 models
> show #!175 models
> hide #!175 models
> show #!174 models
> hide #!174 models
> show #!173 models
> hide #!173 models
> show #!172 models
> hide #!172 models
> show #!171 models
> hide #!171 models
> open 6SKL fromDatabase pdb format mmcif
6skl title:
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
Conformation 1 [more info...]
Chain information for 6skl #177
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | DNA fork, leading-strand template |
J | DNA fork, lagging-strand template |
X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
Non-standard residues in 6skl #177
---
ANP \u2014 phosphoaminophosphonic acid-adenylate ester
MG \u2014 magnesium ion
ZN \u2014 zinc ion
> lighting simple
> select /2
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> select /6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select /4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select /5
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
\u2014\u2014\u2014 End of log from Fri Jun 21 11:35:11 2024 \u2014\u2014\u2014
opened ChimeraX session
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select subtract #177
Nothing selected
> hide #!177 models
> show #!174 models
> hide #!174 models
> show #!166 models
> show #!167 models
> hide #!166 models
> show #!166 models
> hide #!167 models
> show #!167 models
> hide #!166 models
> show #!166 models
> hide #!167 models
> hide #!166 models
> show #!166 models
> show #!172 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!172 models
> hide #!166 models
> show #!172 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
Opened cryosparc_P17_J721_006_volume_map.mrc as #158, grid size 294,294,294,
pixel 1.9, shown at level 0.346, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J719_007_volume_map.mrc
Opened cryosparc_P17_J719_007_volume_map.mrc as #178, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J717_007_volume_map.mrc
Opened cryosparc_P17_J717_007_volume_map.mrc as #179, grid size 294,294,294,
pixel 1.9, shown at level 0.35, step 2, values float32
> hide #!172 models
> show #!172 models
> hide #!172 models
> volume #179 step 1
> volume #178 step 1
> volume #178 level 0.4299
> volume #158 step 1
> close #158
> close #179
> close #178
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map_sharp.mrc
Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
294,294,294, pixel 1.9, shown at level 0.35, step 2, values float32
> volume #158 step 1
> volume #158 level 0.4035
> volume #158 level 0.3381
> show #!172 models
> show #!166 models
> hide #!172 models
> hide #!166 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #178 step 1
> volume #178 level 0.5544
> volume #178 level 0.3502
> close #178
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #178 step 1
> volume #178 level 0.9947
> volume #179 step 1
> volume #179 level 0.1617
> volume #179 level 0.152
> show #!172 models
> hide #!172 models
> lighting soft
> volume #179 level 0.1695
> hide #!179 models
> show #!172 models
> volume #172 level 0.3737
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!166 models
> show #!166 models
> hide #!172 models
> volume #166 level 0.3843
> show #!172 models
> hide #!172 models
> show #!172 models
> hide #!172 models
> show #!172 models
> hide #!166 models
> hide #!172 models
> show #!178 models
> hide #!178 models
> show #!172 models
> volume #172 level 0.3509
> show #!171 models
> hide #!171 models
> hide #!172 models
> show #!179 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
Opened cryosparc_P17_J709_007_volume_map.mrc as #180, grid size 294,294,294,
pixel 1.9, shown at level 0.354, step 2, values float32
> hide #!179 models
> hide #!180 models
> close #180
> open /Users/cvetkom/Downloads/cryosparc_P17_J787_004_volume_map_sharp.mrc
Opened cryosparc_P17_J787_004_volume_map_sharp.mrc as #180, grid size
588,588,588, pixel 0.95, shown at level 0.196, step 4, values float32
> volume #180 level 0.3198
> volume #180 step 1
> volume #180 level 0.4233
> volume #180 level 0.4003
> open /Users/cvetkom/Downloads/cryosparc_P17_J786_005_volume_map_sharp.mrc
Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
588,588,588, pixel 0.95, shown at level 0.204, step 4, values float32
> volume #181 step 1
> volume #181 level 0.3442
> volume #181 level 0.4
> open /Users/cvetkom/Downloads/cryosparc_P17_J787_005_volume_map_sharp.mrc
Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
588,588,588, pixel 0.95, shown at level 0.21, step 4, values float32
> hide #!181 models
> volume #182 step 1
> volume #182 level 0.3526
> volume #182 level 0.4
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job690/mask.mrc
Opened mask.mrc as #183, grid size 588,588,588, pixel 0.95, shown at level 1,
step 4, values float32
> close #183
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map_sharp.mrc
Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
pixel 0.95, shown at level 0.153, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_mask_fsc.mrc
Opened cryosparc_P17_J792_volume_mask_fsc.mrc as #184, grid size 520,520,520,
pixel 0.95, shown at level 5e-05, step 4, values float32
> hide #!182 models
> volume #183 step 1
> volume #183 level 0.3916
> lighting soft
> lighting full
> volume #184 step 1
> volume #184 level 1
> volume #184 color #b2b2ff80
> volume #184 level 0
> volume #184 level 0.03512
> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
Opened cryosparc_P17_J760_mask(1).mrc as #185, grid size 520,520,520, pixel
0.95, shown at level 5e-05, step 4, values float32
> volume #185 step 1
> volume #185 color #ffb2ff7f
> volume #185 level 1
[Repeated 1 time(s)]
> open /Users/cvetkom/Downloads/cryosparc_P17_J757_volume_map.mrc
Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
0.95, shown at level 0.0189, step 4, values float32
> volume #186 level 0.07565
> volume #186 step 1
> hide #!183 models
> hide #!185 models
> volume #186 level 0.1989
> volume #186 level 0.1509
> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map.mrc
Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
0.95, shown at level 0.0388, step 4, values float32
> hide #!183 models
> hide #!186 models
> volume #187 level 0.0929
> volume #187 step 1
> volume #187 level 0.2473
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!186 models
> volume #186 level 0.1781
> hide #!186 models
> show #!186 models
> hide #!186 models
> show #!186 models
> volume #186 level 0.2261
> hide #!186 models
> show #!186 models
> hide #!186 models
> show #!184 models
> show #!185 models
> volume #184 level 1
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!183 models
> hide #!183 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map.mrc
Opened cryosparc_P17_J795_007_volume_map.mrc as #188, grid size 520,520,520,
pixel 0.95, shown at level 0.0131, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map_sharp.mrc
Opened cryosparc_P17_J795_007_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.0597, step 4, values float32
> hide #!184 models
> hide #!187 models
> volume #188 level 0.1056
> volume #188 step 1
> volume #188 level 0.2671
> volume #188 level 0.2362
> volume #189 level 0.3385
> volume #189 step 1
> close #188-189
> close #185
> close #184
> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map_sharp.mrc
Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
520,520,520, pixel 0.95, shown at level 0.213, step 4, values float32
> volume #184 level 0.4718
> volume #184 step 1
> volume #184 level 0.7484
> volume #184 level 0.846
> show #!183 models
> hide #!183 models
> show #!183 models
> hide #!183 models
> show #!183 models
> hide #!183 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map.mrc
Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
pixel 0.95, shown at level 0.0436, step 4, values float32
> hide #!185 models
> show #!185 models
> hide #!184 models
> volume #185 level 0.2092
> volume #185 step 1
> volume #185 level 0.2795
> lighting soft
> volume #185 level 0.2092
> volume #185 level 0.08268
> volume #185 level 0.1858
> volume #185 level 0.1904
> volume #185 level 0.2279
> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
0.95, shown at level 5e-05, step 4, values float32
> volume #188 step 1
> volume #188 level 0.9982
> volume #188 color #ffffb280
> volume #188 color #ffffb266
> volume #185 level 0.2607
> show #!183 models
> hide #!183 models
> show #!183 models
> show #!182 models
> hide #!182 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!183 models
> volume #185 level 0.256
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!180 models
> hide #!180 models
> show #!177 models
> hide #!177 models
> show #!178 models
> hide #!178 models
> show #!179 models
> hide #!179 models
> show #!180 models
> show #!182 models
> hide #!182 models
> close #180
> show #!181 models
> hide #!181 models
> show #!179 models
> hide #!179 models
> show #!181 models
> hide #!181 models
> show #!182 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> show #!181 models
> hide #!181 models
> show #!181 models
> hide #!182 models
> show #!179 models
> hide #!179 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!181 models
> show #!183 models
> hide #!183 models
> show #!184 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!184 models
> volume #185 level 0.2841
> show #!184 models
> volume #184 level 0.7159
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!185 models
> show #!185 models
> hide #!182 models
> volume #185 level 0.3076
> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map.mrc
Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
pixel 0.95, shown at level 0.0442, step 4, values float32
> hide #!185 models
> volume #180 level 0.09552
> volume #180 step 1
> volume #180 level 0.2625
> show #!182 models
> hide #!182 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!180 models
> show #!180 models
> hide #!185 models
> volume #180 level 0.2996
> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map_sharp.mrc
Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
520,520,520, pixel 0.95, shown at level 0.217, step 4, values float32
> volume #189 step 1
> volume #189 level 0.3
> volume #189 level 0.7605
> hide #!189 models
> show #!185 models
> volume #185 level 0.31
> volume #180 level 0.31
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> select add #180
2 models selected
> color #180.1 cornflower blue
> select subtract #180
Nothing selected
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> show #!185 models
> hide #!185 models
> hide #!180 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map.mrc
Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
pixel 0.95, shown at level 0.109, step 4, values float32
> volume #190 level 0.1683
> volume #190 step 1
> volume #190 level 0.1911
> volume #190 level 0.3013
> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map_sharp.mrc
Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
588,588,588, pixel 0.95, shown at level 0.211, step 4, values float32
> volume #191 level 0.2508
> volume #191 step 1
> volume #191 level 0.4399
> volume #191 color #005493
> volume #191 color #009193
> select add #191
2 models selected
> ui tool show "Color Actions"
> color sel medium blue
> color sel light sea green
> select subtract #191
Nothing selected
> volume #191 level 0.3926
> show #!182 models
> hide #!182 models
> show #!182 models
> show #!181 models
> hide #!181 models
> hide #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> volume #191 level 0.39
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> show #!182 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> volume #182 level 0.39
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!182 models
> show #!182 models
> hide #!182 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J811_volume_map.mrc
Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
0.95, shown at level 0.00828, step 4, values float32
> hide #!191 models
> volume #192 level 0.03286
> volume #192 step 1
> volume #192 color #4f8f00
> volume #192 color #009051
> volume #192 level 0.07832
> volume #192 level 0.1052
> volume #192 level 0.1
> volume #192 level 0.3
> volume #192 level 0.15
> volume #192 level 0.12
> volume #192 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 5e-05, step 4, values float32
> volume #193 step 1
> volume #193 color #e5bf9980
> volume #193 color #e5bf9967
> volume #193 color #e5bf9966
> volume #193 level 1
> volume #192 level 0.1186
> volume #193 level 0.5009
> volume #193 level 1
> volume #192 level 0.1434
> volume #192 level 0.1217
> close #193
> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
shown at level 5e-05, step 4, values float32
> volume #193 level 1
> volume #193 step 1
> volume #193 color #99bfe574
> volume #193 color #99bfe567
> volume #193 color #99bfe566
> volume #192 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J812_volume_map.mrc
Opened cryosparc_P17_J812_volume_map.mrc as #194, grid size 520,520,520, pixel
0.95, shown at level 0.0198, step 4, values float32
> volume #194 level 0.05264
> volume #194 step 1
> volume #194 level 0.09845
> volume #194 level 0.1
> volume #194 level 0.12
> close #194
> show #!189 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J805_008_volume_map.mrc
Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
pixel 0.95, shown at level 0.0442, step 4, values float32
> hide #!189 models
> volume #194 level 0.2318
> volume #194 step 1
> volume #194 level 0.1158
> volume #194 level 0.3478
> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_00_00116_volume.mrc
Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
336,336,336, pixel 1.47, shown at level 0.0447, step 2, values float32
> hide #!194 models
> volume #195 level 0.2559
> volume #195 step 1
> volume #195 level 0.2828
> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_04_00116_volume.mrc
Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
336,336,336, pixel 1.47, shown at level 0.0135, step 2, values float32
> volume #196 step 1
> volume #196 level 0.1881
> volume #196 level 0.2658
> volume #196 level 0.2887
> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map.mrc
Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
pixel 0.95, shown at level 0.108, step 4, values float32
> hide #!195 models
> hide #!196 models
> volume #197 level 0.1961
> volume #197 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map_sharp.mrc
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
588,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
> volume #198 level 0.3147
> volume #198 step 1
> volume #198 level 0.4907
> volume #198 level 0.46
> volume #198 level 0.4
> volume #198 level 0.36
> volume #198 level 0.46
> open /Users/cvetkom/Downloads/cryosparc_P17_J822_volume_map.mrc
Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
0.95, shown at level 0.121, step 4, values float32
> hide #!199 models
> show #!199 models
> hide #!198 models
> volume #199 step 1
> volume #199 level 0.12
> volume #199 level 0.15
> volume #199 level 0.16
> volume #199 level 0.15
> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> volume #200 step 1
> volume #200 color #b2ffb283
> volume #200 color #b2ffb26c
> volume #200 color #b2ffb26b
> volume #200 level 1
> close #200
> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> color #200 #e5bf996b models
> color #200 #e5bf9968 models
> color #200 #e5bf9967 models
> color #200 #e5bf9966 models
> volume #200 step 1
> volume #200 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J824_005_volume_map_sharp.mrc
Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
588,588,588, pixel 0.95, shown at level 0.191, step 4, values float32
> hide #!200 models
> hide #!199 models
> volume #201 level 0.4868
> volume #201 step 1
> volume #201 level 0.46
> volume #201 level 0.4
> volume #201 level 0.38
> volume #201 level 0.3
> volume #201 level 0.32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class001.mrc
Opened Cl3D_j718_run_it025_class001.mrc as #202, grid size 520,520,520, pixel
0.95, shown at level 7.31e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class002.mrc
Opened Cl3D_j718_run_it025_class002.mrc as #203, grid size 520,520,520, pixel
0.95, shown at level 6.19e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class003.mrc
Opened Cl3D_j718_run_it025_class003.mrc as #204, grid size 520,520,520, pixel
0.95, shown at level 5.74e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class004.mrc
Opened Cl3D_j718_run_it025_class004.mrc as #205, grid size 520,520,520, pixel
0.95, shown at level 1.81e-06, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class005.mrc
Opened Cl3D_j718_run_it025_class005.mrc as #206, grid size 520,520,520, pixel
0.95, shown at level 5.25e-07, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class006.mrc
Opened Cl3D_j718_run_it025_class006.mrc as #207, grid size 520,520,520, pixel
0.95, shown at level 2.64e-07, step 4, values float32
> hide #!201 models
> hide #!203 models
> hide #!204 models
> hide #!205 models
> hide #!206 models
> hide #!207 models
> volume #202 step 1
> volume #202 level 0.001537
> volume #203 step 1
> volume #203 level 0.00429
> hide #!203 models
> show #!205 models
> volume #205 step 1
> volume #205 level 0.006238
> volume #205 level 0.007973
> hide #!205 models
> show #!205 models
> hide #!205 models
> volume #206 step 1
> volume #206 level 0.003432
> volume #206 level 0.004328
> volume #202 level 0.001682
> show #!205 models
> hide #!205 models
> show #!205 models
> hide #!205 models
> volume #202 level 0.001267
> volume #203 level 0.004002
> volume #204 step 1
> volume #204 level 0.004153
> volume #204 level 0.003947
> volume #206 level 0.004481
> volume #207 step 1
> volume #207 level 0.00211
> hide #!207 models
> show #!205 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J828_volume_map.mrc
Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
0.95, shown at level 0.14, step 4, values float32
> hide #!205 models
> volume #208 step 1
> volume #208 level 0.1685
> volume #208 level 0.1611
> volume #208 level 0.08448
> open /Users/cvetkom/Downloads/cryosparc_P17_J829_class_00_final_volume.mrc
Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
192,192,192, pixel 2.91, shown at level 0.585, step 1, values float32
> hide #!208 models
> volume #209 level 0.5
> volume #209 level 0.4
> volume #209 level 0.45
> volume #209 level 0.5
> open /Users/cvetkom/Downloads/cryosparc_P17_J830_mask.mrc
Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
shown at level 1, step 1, values float32
> volume #210 color #e5bf9975
> volume #210 color #e5bf9967
> volume #210 color #e5bf9966
> volume #210 level 1
[Repeated 1 time(s)]
> hide #!210 models
> hide #!209 models
> show #!201 models
> hide #!201 models
> show #!201 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J825_006_volume_map_sharp.mrc
Opened cryosparc_P17_J825_006_volume_map_sharp.mrc as #211, grid size
588,588,588, pixel 0.95, shown at level 0.189, step 4, values float32
> volume #211 step 1
> volume #211 level 0.3194
> volume #211 level 0.32
> hide #!201 models
> show #!201 models
> hide #!201 models
> show #!201 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> color #211 #ff40ffff models
> color #211 #7a81ffff models
> hide #!201 models
> show #!201 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> show #!202 models
> hide #!201 models
> hide #!202 models
> volume #211 level 0.35
> show #!201 models
> hide #!211 models
> volume #201 level 0.35
> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_map_sharp.mrc
Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
588,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
> hide #!201 models
> volume #212 level 0.4011
> volume #212 step 1
> show #!201 models
> hide #!201 models
> show #!211 models
> hide #!211 models
> show #!211 models
> select add #211
2 models selected
> ui mousemode right "rotate selected models"
Drag select of 211 cryosparc_P17_J825_006_volume_map_sharp.mrc , 212
cryosparc_P17_J831_007_volume_map_sharp.mrc
> select subtract #212
2 models selected
> view matrix models
> #211,0.99974,0.0073342,0.021665,-7.9265,-0.0059368,0.99794,-0.063871,19.839,-0.022089,0.063726,0.99772,-10.804
> view matrix models
> #211,-0.83053,-0.50843,-0.22743,701.17,-0.55206,0.80558,0.21509,144.3,0.073856,0.30419,-0.94974,435.51
> select subtract #211
Nothing selected
> ui tool show "Fit in Map"
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
correlation = 0.5456, correlation about mean = 0.05943, overlap = 5.974e+04
steps = 436, shift = 6.8, angle = 10.9 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.89957058 -0.40667531 -0.15933603 680.38831906
-0.42615436 0.89716922 0.11610278 108.46539449
0.09573525 0.17234438 -0.98037349 475.76940193
Axis 0.21472534 -0.97383892 -0.07436926
Axis point 336.07482386 0.00000000 256.67979639
Rotation angle (degrees) 172.47482888
Shift along axis 5.08617368
Correlation = 0.5456, Correlation about mean = 0.05943, Overlap = 5.974e+04
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
correlation = 0.5457, correlation about mean = 0.0594, overlap = 5.974e+04
steps = 44, shift = 0.0378, angle = 0.0389 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.89980651 -0.40634880 -0.15883608 680.25943553
-0.42572683 0.89739120 0.11595559 108.32590029
0.09541969 0.17195838 -0.98047203 475.96728322
Axis 0.21451210 -0.97389690 -0.07422527
Axis point 336.02953423 0.00000000 256.71123961
Rotation angle (degrees) 172.49947586
Shift along axis 5.09681985
> select add #211
2 models selected
> view matrix models
> #211,-0.90089,-0.40799,-0.14811,678.04,-0.41938,0.90616,0.054752,121.11,0.11187,0.11144,-0.98745,489.99
> volume #211 level 0.4
> select subtract #211
Nothing selected
> fitmap #211 inMap #212
Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
cryosparc_P17_J831_007_volume_map_sharp.mrc using 381853 points
correlation = 0.9767, correlation about mean = 0.8803, overlap = 1.862e+05
steps = 388, shift = 8.54, angle = 19 degrees
Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
Matrix rotation and translation
-0.97678811 -0.20990860 -0.04270100 623.15903654
-0.20103231 0.96714269 -0.15563105 99.70859450
0.07396625 -0.14343428 -0.98689189 576.21341964
Axis 0.10368016 -0.99174448 0.07545400
Axis point 308.25071118 0.00000000 301.13328663
Rotation angle (degrees) 176.62796126
Shift along axis 9.20139044
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!211 models
> volume #212 level 0.4
> volume #212 level 0.38
> volume #212 level 0.35
> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_mask_refine.mrc
Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
588,588,588, pixel 0.95, shown at level 1, step 4, values float32
> volume #213 color #b2b2b259
> volume #213 step 1
> volume #213 level 1
> volume #212 level 0.2391
> close #211
> open /Users/cvetkom/Downloads/cryosparc_P17_J843_008_volume_map_sharp.mrc
Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
520,520,520, pixel 0.95, shown at level 0.249, step 4, values float32
> hide #!211 models
> hide #!212 models
> hide #!213 models
> show #!211 models
> volume #211 level 0.7129
> volume #211 step 1
> volume #211 level 0.5829
> volume #211 level 0.56
> volume #211 level 0.55
> volume #211 level 0.5
> show #!194 models
> hide #!194 models
> show #!189 models
> hide #!189 models
> show #!189 models
> hide #!189 models
> show #!189 models
> hide #!189 models
> volume #211 level 0.55
> show #!189 models
> hide #!189 models
> show #!189 models
> volume #189 level 0.6
> hide #!189 models
> show #!189 models
> hide #!189 models
> ui mousemode right zoom
> hide #!211 models
> show #!210 models
> hide #!210 models
> show #!202 models
> hide #!202 models
> show #!203 models
> hide #!203 models
> show #!204 models
> hide #!204 models
> show #!205 models
> hide #!205 models
> show #!206 models
> hide #!206 models
> show #!207 models
> close #202-207
> show #!176 models
> hide #!176 models
> show #!129 models
> hide #!129 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> show #!135 models
> hide #!134 models
> hide #!133 models
> show #!133 models
> hide #!135 models
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> hide #!133 models
> show #!133 models
> show #!134 models
> hide #!134 models
> hide #!133 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!131 models
> hide #!131 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!110 models
> show #!111 models
> hide #!110 models
> hide #!111 models
> show #!112 models
> show #!120 models
> hide #!120 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!112 models
> show #!112 models
> hide #!133 models
> show #!134 models
> hide #!112 models
> show #!113 models
> hide #!113 models
> show #!113 models
> hide #!113 models
> show #!110 models
> hide #!110 models
> show #!111 models
> hide #!111 models
> show #!112 models
> hide #!112 models
> show #!113 models
> hide #!113 models
> show #!114 models
> hide #!114 models
> show #!115 models
> hide #!115 models
> show #!115 models
> hide #!115 models
> show #!115 models
> hide #!115 models
> hide #!134 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!71 models
> hide #!71 models
> show #!130 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> hide #!130 models
> show #!110 models
> show #!98 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!98 models
> show #!98 models
> hide #!110 models
> hide #!98 models
> show #!105 models
> show #!106 models
> hide #!105 models
> hide #!106 models
> show #!117 models
> show #!118 models
> hide #!117 models
> hide #!118 models
> show #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!70 models
> show #!71 models
> hide #!70 models
> show #!70 models
> hide #!70 models
> show #!70 models
> hide #!71 models
> show #!72 models
> hide #!72 models
> show #!73 models
> hide #!73 models
> show #!73 models
> hide #!73 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!70 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> show #!74 models
> hide #!74 models
> show #!75 models
> hide #!75 models
> show #!130 models
> hide #!130 models
> show #!130 models
> show #!98 models
> hide #!98 models
> hide #!130 models
> show #!130 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!130 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> show #!129 models
> show #!130 models
> hide #!98 models
> hide #!99 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!139 models
> hide #!139 models
> show #!139 models
> hide #!139 models
> show #!139 models
> hide #!130 models
> show #!138 models
> hide #!139 models
> show #!143 models
> hide #!143 models
> show #!143 models
> hide #!138 models
> hide #!143 models
> show #!141 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> hide #!147 models
> show #!140 models
> hide #!140 models
> show #!145 models
> show #!146 models
> hide #!146 models
> show #!146 models
> hide #!145 models
> hide #!146 models
> show #!148 models
> hide #!148 models
> show #!157 models
> hide #!157 models
> show #!161 models
> hide #!161 models
> show #!174 models
> hide #!174 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
pixel 1.9, shown at level 0.346, step 2, values float32
> volume #202 step 1
> volume #202 level 0.3331
> show #!157 models
> hide #!157 models
> show #!157 models
> hide #!157 models
> show #!161 models
> volume #161 level 0.32
> volume #161 level 0.34
> hide #!161 models
> show #!160 models
> hide #!160 models
> show #!159 models
> show #!161 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> hide #!159 models
> show #!159 models
> hide #!159 models
> show #!160 models
> show #!173 models
> show #!175 models
> show #!157 models
> hide #!157 models
> hide #!160 models
> volume #173 level 0.3031
> volume #173 level 0.3465
> show #!175 models
> hide #!173 models
> volume #175 level 0.3281
> hide #!175 models
> show #!172 models
> hide #!172 models
> close #155-156,159-160,173,175-176
> show #!157 models
> show #!174 models
> hide #!174 models
> show #!174 models
> volume #174 level 0.3294
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> show #!174 models
> hide #!174 models
> hide #!157 models
> show #!161 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> show #!161 models
> select add #161
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #161,-0.80087,-0.4765,-0.3627,729.62,0.10949,-0.71198,0.69361,276.28,-0.58874,0.51578,0.62238,115.15
> view matrix models
> #161,-0.84255,0.43705,-0.31481,469.51,-0.49419,-0.85972,0.12908,627.85,-0.21423,0.26433,0.94034,2.6659
> view matrix models
> #161,-0.91542,-0.17496,-0.36248,675.94,0.17298,-0.98418,0.038186,498.42,-0.36343,-0.027746,0.93121,129.94
> view matrix models
> #161,-0.95897,-0.26467,-0.1016,649.01,0.27072,-0.9613,-0.051053,486.58,-0.084153,-0.076463,0.99351,49.911
> view matrix models
> #161,-0.99187,0.12321,0.03177,514.81,-0.12543,-0.98874,-0.081553,613.22,0.021365,-0.084875,0.99616,22.011
> ui mousemode right zoom
> select clear
> hide #!161 models
> show #!161 models
> fitmap #161 inMap #141
Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
cryosparc_P17_J685_007_volume_map.mrc using 269413 points
correlation = 0.9961, correlation about mean = 0.9593, overlap = 9.415e+04
steps = 112, shift = 3.83, angle = 9.13 degrees
Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
Matrix rotation and translation
-0.99974072 -0.02276472 -0.00050563 565.44941758
0.02276965 -0.99929232 -0.02994005 559.04447071
0.00017631 -0.02994380 0.99955157 8.32772983
Axis -0.00008235 -0.01497460 0.99988787
Axis point 279.54196619 282.80415641 0.00000000
Rotation angle (degrees) 178.69527744
Shift along axis -0.09123841
> hide #!141 models
> show #!141 models
> volume #161 level 0.36
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!141 models
> show #!147 models
> hide #!141 models
> show #!141 models
> hide #!141 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!161 models
> show #!161 models
> hide #!161 models
> show #!141 models
> select add #147
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #147,0.75391,-0.62474,-0.20327,302.4,-0.65039,-0.66601,-0.36528,749.91,0.092824,0.40759,-0.90843,455.15
> view matrix models
> #147,-0.31245,-0.67282,-0.67059,759.97,-0.54055,0.70643,-0.45691,373.58,0.78114,0.21972,-0.58441,212.49
> view matrix models
> #147,-0.90083,-0.32948,-0.28274,711.29,-0.41209,0.85388,0.3179,56.872,0.13669,0.40289,-0.90498,443.04
> view matrix models
> #147,-0.99864,0.030742,-0.042093,565.93,0.029267,0.99895,0.035202,-18.858,0.043131,0.033922,-0.99849,598.86
> ui mousemode right "translate selected models"
> view matrix models
> #147,-0.99864,0.030742,-0.042093,560.75,0.029267,0.99895,0.035202,-44.757,0.043131,0.033922,-0.99849,550.76
> view matrix models
> #147,-0.99864,0.030742,-0.042093,571.25,0.029267,0.99895,0.035202,-21.366,0.043131,0.033922,-0.99849,539.43
> select subtract #147
Nothing selected
> fitmap #147 inMap #141
Fit map cryosparc_P17_J690_006_volume_map.mrc in map
cryosparc_P17_J685_007_volume_map.mrc using 254434 points
correlation = 0.9983, correlation about mean = 0.9814, overlap = 9.297e+04
steps = 84, shift = 10.7, angle = 2.98 degrees
Position of cryosparc_P17_J690_006_volume_map.mrc (#147) relative to
cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
Matrix rotation and translation
-0.99966375 0.02590789 -0.00108426 552.09827323
0.02590403 0.99965851 0.00344015 -9.28972053
0.00117301 0.00341091 -0.99999349 555.06217083
Axis -0.01295398 -0.99991463 -0.00171281
Axis point 275.95266832 0.00000000 277.69485205
Rotation angle (degrees) 179.93532851
Shift along axis 1.18634199
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!141 models
> show #!157 models
> hide #!157 models
> show #!161 models
> hide #!161 models
> show #!161 models
> color #161 #00fa92ff models
> hide #!161 models
> show #!161 models
> hide #!147 models
> show #!147 models
> hide #!147 models
> show #!147 models
> hide #!161 models
> hide #!147 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> hide #!32 models
> show #!32 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> ui mousemode right zoom
> lighting full
> lighting soft
> lighting simple
> lighting full
> hide #!32 models
> show #!32 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!95 models
> hide #!95 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J517_006_volume_map_zflip.mrc
Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #155 step 1
> lighting soft
> show #!179 models
> hide #!179 models
> show #!179 models
> hide #!179 models
> show #!179 models
> select add #155
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #155,-0.98089,0.19377,-0.017464,502.92,0.10481,0.60192,0.79165,-107.18,0.16391,0.77469,-0.61072,122.66
> view matrix models
> #155,-0.25052,0.96798,-0.015979,76.052,0.96671,0.24923,-0.057953,-41.024,-0.052115,-0.029966,-0.99819,507.99
> view matrix models
> #155,0.96775,0.17696,-0.17931,1.7558,0.20922,-0.96102,0.18073,460.27,-0.14034,-0.21242,-0.96705,577.47
> view matrix models
> #155,0.96767,0.091902,-0.2349,39.67,0.12427,-0.9841,0.12691,503.72,-0.2195,-0.152,-0.9637,581.47
> view matrix models
> #155,0.91176,0.40771,0.049574,-104.32,0.37999,-0.79159,-0.47852,523.82,-0.15586,0.45514,-0.87667,368.35
> lighting simple
> view matrix models
> #155,0.92481,0.37946,0.027133,-94.419,0.34082,-0.79474,-0.50223,541.44,-0.16901,0.47372,-0.86431,363.7
> view matrix models
> #155,0.94675,0.28168,0.15598,-103.76,0.32196,-0.82268,-0.46855,546.56,-0.0036582,0.49382,-0.86956,312.94
> view matrix models
> #155,0.9947,0.045724,-0.092058,10.698,0.043566,-0.99873,-0.02532,567.43,-0.093098,0.021175,-0.99543,504.12
> ui mousemode right "translate selected models"
> view matrix models
> #155,0.9947,0.045724,-0.092058,46.226,0.043566,-0.99873,-0.02532,564.24,-0.093098,0.021175,-0.99543,557.75
> view matrix models
> #155,0.9947,0.045724,-0.092058,13.547,0.043566,-0.99873,-0.02532,566.45,-0.093098,0.021175,-0.99543,563.81
> select subtract #155
Nothing selected
> fitmap #155 inMap #179
Fit map cryosparc_P17_J517_006_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2026669 points
correlation = 0.9972, correlation about mean = 0.9729, overlap = 1.474e+05
steps = 220, shift = 19.3, angle = 6.44 degrees
Position of cryosparc_P17_J517_006_volume_map_zflip.mrc (#155) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#179) coordinates:
Matrix rotation and translation
0.99982429 0.01272017 0.01376969 -7.71473943
0.01281628 -0.99989397 -0.00691402 556.62008375
0.01368028 0.00708928 -0.99988130 552.40010778
Axis 0.99995607 0.00638455 0.00686279
Axis point 0.00000000 277.36764127 277.20094376
Rotation angle (degrees) 179.59881412
Shift along axis -0.36962502
> ui mousemode right zoom
> lighting soft
> hide #!179 models
> show #!179 models
> hide #!179 models
> show #!179 models
> show #!178 models
> hide #!179 models
> show #!179 models
> hide #!178 models
> volume #179 level 0.16
> hide #!179 models
> show #!179 models
> hide #!179 models
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J851_volume_map.mrc
Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
0.95, shown at level 0.179, step 4, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J854_volume_map.mrc
Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
0.95, shown at level 0.178, step 4, values float32
> hide #!156 models
> show #!156 models
> hide #!156 models
> hide #!159 models
> show #!159 models
> show #!156 models
> volume #156 step 1
> volume #159 step 1
> volume #156 level 0.15
> volume #159 level 0.15
> volume #156 level 0.12
> volume #156 level 0.1
> open /Users/cvetkom/Downloads/cryosparc_P17_J857_mask.mrc
Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
shown at level 1, step 4, values float32
> volume #160 step 1
> volume #160 color #b2ffb260
> volume #160 color #b2ffb261
> volume #160 level 1
> volume #160 color #b2ffb270
> volume #160 level 1
> volume #156 level 0.08
> volume #156 level 0.1
> volume #156 level 0.9
> volume #156 level 0.09
> volume #156 level 0.08
> open /Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
pixel 0.95, shown at level 0.154, step 4, values float32
> volume #173 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J866_class_00_00042_volume.mrc
Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
128,128,128, pixel 4.36, shown at level 1.71, step 1, values float32
> volume #175 level 1.364
> volume #175 level 1
> volume #175 level 0.9
> volume #175 level 0.8
> volume #175 level 0.9
> open /Users/cvetkom/Downloads/cryosparc_P17_J869_mask.mrc
Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #176 color #cccc9964
> volume #176 color #cccc9963
> volume #176 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J870_mask.mrc
Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #203 color #b2b2b267
> volume #203 color #b2b2b266
> volume #203 level 1
[Repeated 1 time(s)]
> show #!213 models
> hide #!213 models
> show #!213 models
> hide #!213 models
> hide #!203 models
> show #!203 models
> hide #!203 models
> show #!211 models
> hide #!211 models
> show #!212 models
> hide #!212 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J867_007_volume_map.mrc
Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J871_007_volume_map.mrc
Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> volume #204 step 1
> volume #205 step 1
> volume #205 level 0.2369
> volume #205 level 0.1513
> show #!130 models
> hide #!130 models
> show #!130 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> volume #129 level 0.01525
> volume #129 level 0.02295
> volume #129 level 0.02195
> volume #129 level 0.02859
> volume #129 level 0.01548
> volume #129 level 0.01394
> volume #129 level 0.02201
> volume #129 level 0.02491
> volume #129 level 0.02207
> volume #129 level 0.01258
> volume #129 level 0.01323
> show #!74 models
> volume #129 level 0.014
> hide #!74 models
> show #!74 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> hide #!75 models
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!98 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!122 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!122 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> hide #!123 models
> show #!122 models
> show #!123 models
> hide #!122 models
> show #!122 models
> show #!124 models
> hide #!123 models
> hide #!122 models
> hide #!124 models
> show #!124 models
> show #!123 models
> hide #!123 models
> show #!122 models
> hide #!122 models
> hide #!124 models
> show #!124 models
> hide #!124 models
> show #!125 models
> hide #!125 models
> show #!125 models
> hide #!125 models
> show #!126 models
> show #!127 models
> show #!134 models
> show #!135 models
> hide #!135 models
> show #!128 models
> hide #!128 models
> show #!135 models
> hide #!135 models
> show #!133 models
> hide #!127 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!126 models
> hide #!126 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> show #!127 models
> hide #!127 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> show #!133 models
> hide #!133 models
> hide #!134 models
> show #!129 models
> show #!130 models
> show #!131 models
> hide #!131 models
> show #!132 models
> hide #!132 models
> show #!132 models
> hide #!132 models
> show #!133 models
> show #!134 models
> show #!132 models
> hide #!132 models
> show #!131 models
> hide #!131 models
> hide #!133 models
> hide #!134 models
> show #!122 models
> show #!123 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!130 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> hide #!130 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!133 models
> show #!134 models
> show #!104 models
> hide #!104 models
> show #!103 models
> hide #!103 models
> show #!103 models
> show #!102 models
> hide #!102 models
> show #!104 models
> hide #!104 models
> show #!102 models
> hide #!103 models
> show #!103 models
> hide #!102 models
> show #!101 models
> hide #!101 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!103 models
> show #!103 models
> hide #!100 models
> show #!100 models
> hide #!133 models
> hide #!134 models
> show #!134 models
> hide #!134 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!103 models
> show #!103 models
> hide #!103 models
> show #!103 models
> hide #!103 models
> show #!103 models
> hide #!100 models
> hide #!103 models
> show #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> show #!100 models
> hide #!100 models
> show #!101 models
> hide #!101 models
> show #!102 models
> hide #!102 models
> show #!103 models
> hide #!103 models
> show #!104 models
> hide #!104 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J876_class_00_final_volume.mrc
Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
192,192,192, pixel 2.91, shown at level 0.504, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J880_class_00_final_volume.mrc
Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
192,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
> hide #!98 models
> hide #!99 models
> hide #!129 models
> hide #!130 models
> volume #206 level 0.3476
> open /Users/cvetkom/Downloads/cryosparc_P17_J874_volume_map.mrc
Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
1.9, shown at level 0.404, step 2, values float32
> volume #214 step 1
> volume #214 level 0.3304
> open /Users/cvetkom/Downloads/cryosparc_P17_J882_volume_map.mrc
Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
1.9, shown at level 0.4, step 2, values float32
> volume #215 step 1
> volume #215 level 0.347
> volume #215 level 0.3003
> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_00_00042_volume.mrc
Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
128,128,128, pixel 4.36, shown at level 0.839, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_01_00042_volume.mrc
Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
128,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
> volume #216 level 1.25
> volume #217 level 1.171
> volume #217 level 1
> volume #217 level 0.9
> volume #217 level 0.8
> volume #217 level 0.85
> volume #217 level 0.8
> open /Users/cvetkom/Downloads/cryosparc_P17_J883_mask.mrc
Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
shown at level 1, step 1, values float32
> volume #218 color #cccc9967
> volume #218 color #cccc9969
> volume #218 level 1
> volume #218 level 0.5107
> volume #218 level 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J885_008_volume_map.mrc
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> hide #!217 models
> hide #!218 models
> volume #219 step 1
> volume #220 step 1
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc
Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
0.95, shown at level 0.00502, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc
Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
0.95, shown at level 0.00208, step 4, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job519.mrc
Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
level 5e-05, step 4, values float32
> hide #!218 models
> hide #!220 models
> volume #223 step 1
> volume #223 level 0.9925
> volume #223 color #ffb2ff80
> volume #223 color #ffb2ff66
> volume #222 step 1
> volume #221 step 1
> volume #222 level 0.002458
> volume #222 level 0.003951
> volume #222 level 0.004587
> volume #222 level 0.005
> volume #222 level 0.004508
> volume #222 level 0.0045
> volume #221 level 0.0045
> hide #!223 models
> hide #!221 models
> show #!221 models
> hide #!222 models
> hide #!221 models
> show #!222 models
> ui tool show "Map Eraser"
> hide #224 models
> show #224 models
> hide #!222 models
Drag select of eraser sphere, 87 of 1000 triangles
> select clear
> show #!222 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> ui mousemode right zoom
> select add #224
1 model selected
> ui mousemode right "translate selected models"
> hide #224 models
> show #224 models
> hide #!222 models
> show #!222 models
> select subtract #224
Nothing selected
> select add #224
1 model selected
> select subtract #224
Nothing selected
> ui mousemode right zoom
Drag select of eraser sphere, 27 of 1000 triangles
> select #224
1 model selected
> select #224
1 model selected
> select clear
> ui mousemode right "map eraser"
> volume erase #222 center 235.13,229.91,259.65 radius 50.358
Opened Ref3D_job506_run_class001_NCP.mrc copy as #225, grid size 588,588,588,
pixel 0.95, shown at step 1, values float32
> volume erase #225 center 240.34,217.6,249.39 radius 50.274
> volume erase #225 center 249.31,217.92,185.58 radius 50.274
> volume erase #225 center 254.34,196.31,201.83 radius 50.274
> volume erase #225 center 244.51,226.1,178.85 radius 50.274
> volume erase #225 center 266.29,219.21,231.39 radius 71.221
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> ui mousemode right zoom
> vop gaussian #225 sdev 2.85
Opened Ref3D_job506_run_class001_NCP.mrc copy gaussian as #224, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> volume #224 level 0.004498
> volume #224 level 0.004
> volume #224 level 0.0045
> save
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_bareNCP.mrc
> models #224
> hide #!224 models
> show #!224 models
> show #!222 models
> hide #!222 models
> hide #!225 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!224 models
> show #!224 models
> hide #!224 models
> show #!224 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> lighting full
> hide #!222 models
> show #!222 models
> color #224 #d6d6d6ff models
> color #224 darkgrey models
> hide #!224 models
> show #!224 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> show #!222 models
> hide #!222 models
> hide #!224 models
> show #!222 models
> show #!223 models
> show #!221 models
> volume #223 level 0.5133
> volume #223 level 1
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!224 models
> hide #!222 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> hide #!221 models
> show #!221 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job744/mask.mrc
Opened mask.mrc as #226, grid size 588,588,588, pixel 0.95, shown at level
5e-05, step 4, values float32
> hide #!224 models
> show #!224 models
> hide #!221 models
> volume #226 step 1
> volume #226 color #e5bf9966
> volume #226 level 1
> volume #226 level 0.3859
> volume #226 level 0.5044
> hide #!224 models
> show #!221 models
> volume #226 level 1
> hide #!226 models
> show #!226 models
> volume #226 level 1
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> show #!223 models
> hide #!223 models
> volume #226 level 1
> hide #!221 models
> hide #!226 models
> show #!219 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> close #219-220
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J884_009_volume_map.mrc
Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J885_008_volume_map.mrc
Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
pixel 1.9, shown at level 0.347, step 2, values float32
> volume #219 step 1
> volume #220 step 1
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J888_009_volume_map.mrc
Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 2, values float32
> volume #227 step 1
> volume #219 level 0.4485
> volume #219 level 0.4625
> volume #219 step 2
> volume #219 step 1
> show #!213 models
> hide #!213 models
> volume #227 step 2
> volume #227 step 1
> close #225
> close #226
> hide #!219 models
> show #!219 models
> volume #219 step 2
> volume #219 step 4
> volume #219 step 1
> volume #219 step 2
> volume #219 level 0.4261
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
\u2014\u2014\u2014 End of log from Thu Jul 11 13:31:37 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!219 models
> show #!227 models
> hide #!227 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J984_class_00_00062_volume_sharp.mrc
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
128,128,128, pixel 3.27, shown at level 0.37, step 1, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_00400_volume.mrc
Opened cryosparc_P17_J967_class_00_00400_volume.mrc as #226, grid size
128,128,128, pixel 3.27, shown at level 0.384, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J981_class_00_00062_volume_sharp.mrc
Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
128,128,128, pixel 3.27, shown at level 0.327, step 1, values float32
> show #!227 models
> hide #!227 models
> hide #!225 models
> hide #!228 models
> volume #226 level 1.133
> volume #226 level 1.3
> volume #226 level 1.35
> lighting soft
> volume #226 color darkgrey
> volume #226 level 1.4
> volume #226 level 1.45
> volume #225 level 2.008
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!228 models
> volume #228 level 1.823
> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_final_volume.mrc
Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
192,192,192, pixel 2.18, shown at level 0.197, step 1, values float32
> close #226
> volume #229 level 1.053
> volume #229 level 1
> volume #229 level 0.9
> volume #229 level 0.8
> show #!228 models
> show #!227 models
> hide #!227 models
> show #!225 models
> hide #!229 models
> show #!229 models
> hide #!228 models
> hide #!229 models
> show #!229 models
> volume #225 level 1.9
> volume #225 level 1.8
> hide #!229 models
> show #!229 models
> volume #225 level 1.6
> show #!211 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!198 models
> hide #!198 models
> show #!197 models
> hide #!197 models
> show #!191 models
> hide #!191 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
588,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
588,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
> hide #!225 models
> volume #226 level 0.2956
> volume #226 step 1
> volume #226 level 0.334
> show #!230 models
> hide #!226 models
> volume #226 level 0.33
> show #!226 models
> hide #!230 models
> hide #!226 models
> show #!230 models
> volume #230 step 1
> volume #230 level 0.33
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> volume #230 level 0.32
> volume #230 level 0.3
> show #!226 models
> hide #!226 models
> show #!226 models
> hide #!226 models
> show #!231 models
> hide #!230 models
> volume #231 step 2
> volume #231 step 1
> volume #231 level 0.3
> show #!191 models
> hide #!191 models
> show #!190 models
> show #!191 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!198 models
> hide #!191 models
> open 1ID3 fromDatabase pdb format mmcif
1id3 title:
Crystal structure of the yeast nucleosome core particle reveals fundamental
differences In inter-nucleosome interactions [more info...]
Chain information for 1id3 #232
---
Chain | Description | UniProt
A E | HISTONE H3 | H3_YEAST 1-135
B F | HISTONE H4 | H4_YEAST 1-102
C G | HISTONE H2A.1 | H2A1_YEAST 1-131
D H | HISTONE H2B.2 | H2B2_YEAST 1-130
I J | PALINDROMIC 146BP DNA FRAGMENT |
Non-standard residues in 1id3 #232
---
MN \u2014 manganese (II) ion
> hide #!232 models
> show #!232 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view sel
> select subtract #232
Nothing selected
> show #!228 models
> hide #!228 models
> show #!225 models
> hide #!225 models
> lighting simple
> show #!229 models
> hide #!229 models
> show #!225 models
> show #!228 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!225 models
> show #!225 models
> hide #!228 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #232,1,0,0,194.77,0,1,0,198.7,0,0,1,241.66
> select add #225
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 7 models selected
> view sel
> select subtract #225
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #232,0.45362,0.62002,-0.64016,176.82,-0.86856,0.46844,-0.16176,188.02,0.19958,0.62939,0.75102,238.14
> view matrix models
> #232,0.73516,0.67582,-0.053002,205.68,-0.43197,0.40677,-0.80495,150.64,-0.52244,0.61466,0.59097,235.27
> view matrix models
> #232,0.74922,0.65491,0.098772,212.99,-0.3682,0.53581,-0.75982,154.67,-0.55054,0.53291,0.64258,236.74
> view matrix models
> #232,0.63725,0.62725,-0.44773,185.38,-0.56763,-0.01092,-0.82321,143.6,-0.52125,0.77874,0.34909,225.69
> ui mousemode right "translate selected models"
> view matrix models
> #232,0.63725,0.62725,-0.44773,108.34,-0.56763,-0.01092,-0.82321,126.58,-0.52125,0.77874,0.34909,223.48
> ui mousemode right "rotate selected models"
> view matrix models
> #232,0.69009,0.70479,0.16445,140.62,-0.26062,0.454,-0.85204,130.7,-0.67517,0.54512,0.49698,228.24
> view matrix models
> #232,0.021212,0.98524,0.16984,150.87,-0.50552,0.15714,-0.84839,127.69,-0.86256,-0.067863,0.50139,219.42
> view matrix models
> #232,0.026211,0.99233,-0.12082,136.06,-0.53573,-0.088094,-0.83978,124.17,-0.84398,0.086736,0.52931,223.35
> view matrix models
> #232,0.0051654,0.11484,-0.99337,76.495,-0.63253,-0.76903,-0.092196,151.55,-0.77452,0.62881,0.068669,208.5
> view matrix models
> #232,0.026817,-0.97752,0.20912,119.22,-0.36995,0.18463,0.91052,217.22,-0.92866,-0.10178,-0.35669,175.39
> view matrix models
> #232,-0.0985,-0.93943,0.32829,126.94,0.94539,0.014666,0.32562,174.18,-0.31071,0.34244,0.88668,241.92
> view matrix models
> #232,0.23695,-0.92136,0.30814,123.63,0.84083,0.035592,-0.54013,130.99,0.48669,0.38708,0.78314,231.21
> view matrix models
> #232,0.37181,-0.91507,0.15625,114.91,0.42362,0.017477,-0.90567,115.18,0.82602,0.40293,0.39414,208.93
> view matrix models
> #232,0.30529,-0.94633,-0.10613,101.45,0.56154,0.26891,-0.78253,124.73,0.76907,0.1793,0.6135,216.78
> view matrix models
> #232,0.059237,0.85249,0.51938,166.21,0.47573,-0.48152,0.73609,190.34,0.8776,0.20348,-0.43407,162.69
> view matrix models
> #232,0.24626,-0.51664,-0.82003,72.694,0.61898,0.73489,-0.27712,158.16,0.7458,-0.43934,0.50076,200.59
> view matrix models
> #232,-0.067706,-0.98402,0.16471,117.56,0.51804,-0.17576,-0.83711,114.66,0.85268,0.028649,0.52165,208.85
> volume flip #225
Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip as #233, grid
size 128,128,128, pixel 3.27, shown at step 1, values float32
> view matrix models
> #232,-0.086674,-0.98325,0.16032,117.49,0.60367,-0.17985,-0.77669,117.02,0.79251,0.02946,0.60914,213.81
> view matrix models
> #232,-0.20892,-0.97186,0.10878,115.99,0.81932,-0.11321,0.56205,185.07,-0.53392,0.20655,0.81992,237.89
> view matrix models
> #232,-0.0034667,-0.99986,-0.016272,107.52,0.52919,-0.015641,0.84836,203.66,-0.8485,-0.0056699,0.52917,221.79
> view matrix models
> #232,0.10405,-0.99333,-0.049687,105.09,0.51074,0.010501,0.85967,204.82,-0.85341,-0.11483,0.50843,218.9
> view matrix models
> #232,0.155,-0.97565,0.1552,115.49,0.4679,0.21087,0.85826,208.52,-0.87008,-0.060414,0.48919,218.98
> view matrix models
> #232,0.045605,-0.97983,0.19456,118.28,0.53868,0.18814,0.82123,205.68,-0.84127,0.067353,0.5364,223.36
> ui mousemode right "translate selected models"
> view matrix models
> #232,0.045605,-0.97983,0.19456,194.24,0.53868,0.18814,0.82123,258.89,-0.84127,0.067353,0.5364,231.26
> view matrix models
> #232,0.045605,-0.97983,0.19456,195.08,0.53868,0.18814,0.82123,259.08,-0.84127,0.067353,0.5364,236.86
> ui mousemode right "rotate selected models"
> view matrix models
> #232,-0.039543,-0.99451,0.096893,190.48,-0.23842,0.10356,0.96562,271.04,-0.97036,0.015082,-0.24121,197.13
> view matrix models
> #232,-0.078672,-0.98952,0.12105,192.1,-0.5971,0.14401,0.78913,265.46,-0.7983,-0.010198,-0.60217,176.87
> view matrix models
> #232,-0.14713,-0.98779,0.051262,189.09,-0.8147,0.15042,0.56004,255.52,-0.56091,0.040637,-0.82688,164.4
> select subtract #232
Nothing selected
> ui tool show "Fit in Map"
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 72
shifted from previous position = 12.2
rotated from previous position = 11.2 degrees
atoms outside contour = 5403, contour level = 1.6
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03585182 -0.99591182 0.08291139 194.40297797
-0.72260858 0.08314376 0.68623899 250.19258695
-0.69032709 -0.03530956 -0.72263528 174.98991176
Axis -0.66054809 0.70786809 0.25019790
Axis point 245.81431621 -0.00000000 -10.35559013
Rotation angle (degrees) 146.89506394
Shift along axis 92.47294040
> volume #233 level 1.5
> volume #233 level 1.4
> ui mousemode right "translate selected models"
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view matrix models
> #232,-0.035852,-0.99591,0.082911,187.84,-0.72261,0.083144,0.68624,334.95,-0.69033,-0.03531,-0.72264,195.33
> lighting soft
> view matrix models
> #232,-0.035852,-0.99591,0.082911,189.25,-0.72261,0.083144,0.68624,329.81,-0.69033,-0.03531,-0.72264,193.67
> lighting simple
> view matrix models
> #232,-0.035852,-0.99591,0.082911,207.89,-0.72261,0.083144,0.68624,254.31,-0.69033,-0.03531,-0.72264,174.46
> view matrix models
> #232,-0.035852,-0.99591,0.082911,196.79,-0.72261,0.083144,0.68624,255.92,-0.69033,-0.03531,-0.72264,174.52
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 52
shifted from previous position = 6.21
rotated from previous position = 0.0558 degrees
atoms outside contour = 4425, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03529330 -0.99599473 0.08215154 194.42252609
-0.72248530 0.08222358 0.68647963 250.18011940
-0.69048489 -0.03512516 -0.72249349 174.98679362
Axis -0.66080361 0.70753542 0.25046400
Axis point 245.92146757 -0.00000000 -10.42218197
Rotation angle (degrees) 146.90659877
Shift along axis 92.36408147
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 48
shifted from previous position = 0.0262
rotated from previous position = 0.0179 degrees
atoms outside contour = 4427, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03522647 -0.99601286 0.08196018 194.43601851
-0.72265585 0.08203483 0.68632267 250.16027535
-0.69030980 -0.03505228 -0.72266432 174.97347823
Axis -0.66086507 0.70749095 0.25042747
Axis point 245.92434501 0.00000000 -10.39497167
Rotation angle (degrees) 146.92196206
Shift along axis 92.30832410
> select subtract #232
Nothing selected
> hide #!232 atoms
> show #!232 cartoons
> hide #!233 models
> show #!233 models
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 44
shifted from previous position = 0.00249
rotated from previous position = 0.0128 degrees
atoms outside contour = 4428, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03534401 -0.99599682 0.08210439 194.44302789
-0.72273427 0.08221501 0.68621853 250.15752046
-0.69022169 -0.03508594 -0.72274684 174.96686637
Axis -0.66081898 0.70756214 0.25034793
Axis point 245.90230259 0.00000000 -10.37331191
Rotation angle (degrees) 146.92300591
Shift along axis 92.31293996
> fitmap #232 inMap #233
Fit molecule 1id3 (#232) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
atoms
average map value = 1.802, steps = 48
shifted from previous position = 0.0672
rotated from previous position = 0.0319 degrees
atoms outside contour = 4424, contour level = 1.4
Position of 1id3 (#232) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.03562336 -0.99595084 0.08254033 194.40523233
-0.72285407 0.08271076 0.68603274 250.17963983
-0.69008186 -0.03522582 -0.72287355 174.97000524
Axis -0.66069357 0.70774412 0.25016449
Axis point 245.83818539 0.00000000 -10.32676146
Rotation angle (degrees) 146.91829753
Shift along axis 92.39216339
> volume #233 color #b2b2b2db
> volume #233 color #b2b2b2b0
> volume #233 color #b2b2b29a
> volume #233 color #b2b2b299
> volume #233 color #b2b2b2b2
> volume #233 color #b2b2b2cc
> combine #232
> hide #!232 models
> hide #!234 models
> show #!234 models
> select #234/I
3006 atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
> delete atoms (#!234 & sel)
> delete bonds (#!234 & sel)
> select #234/J
3004 atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
> delete atoms (#!234 & sel)
> delete bonds (#!234 & sel)
> hide #!233 models
> show #!233 models
> fitmap #234 inMap #233
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 6114
atoms
average map value = 1.618, steps = 48
shifted from previous position = 0.869
rotated from previous position = 6.47 degrees
atoms outside contour = 2277, contour level = 1.4
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
Matrix rotation and translation
-0.05927763 -0.99809265 0.01724050 190.79692871
-0.66015313 0.05215041 0.74931847 251.66034038
-0.74878836 0.03303645 -0.66198534 180.19394497
Axis -0.65007489 0.69522355 0.30670320
Axis point 244.94027053 -0.00000000 -21.53118005
Rotation angle (degrees) 146.56966321
Shift along axis 106.19396109
> volume #233 color #b2b2b280
> volume #233 color #b2b2b29a
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!234 models
> hide #!233 models
> show #!233 models
> hide #!232 models
> hide #!233 models
> show #!129 models
> select add #129
4 models selected
> view clip false
> select subtract #129
Nothing selected
> show #!130 models
> show #!227 models
> hide #!227 models
> show #!227 models
> hide #!227 models
> show #!227 models
> hide #!227 models
> volume flip #227
Opened cryosparc_P17_J888_009_volume_map.mrc z flip as #235, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> select add #235
2 models selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #235,0.84663,0.46913,0.25127,-169.59,0.42608,-0.88042,0.20812,364.8,0.31886,-0.069133,-0.94528,519.57
> view matrix models
> #235,-0.53578,-0.80769,-0.24613,731.78,-0.84162,0.48737,0.23271,310.31,-0.067998,0.33183,-0.94089,508.65
> view matrix models
> #235,-0.9965,-0.022294,-0.080596,581.12,-0.043426,0.96162,0.27092,-58.716,0.071463,0.27347,-0.95922,492.67
> ui mousemode right "translate selected models"
> view matrix models
> #235,-0.9965,-0.022294,-0.080596,577.57,-0.043426,0.96162,0.27092,-52.189,0.071463,0.27347,-0.95922,460.39
> volume #235 step 2
> select subtract #235
Nothing selected
> fitmap #235 inMap #130
Fit map cryosparc_P17_J888_009_volume_map.mrc z flip in map
Cl3D_j591_run_it025_class002.mrc using 31742 points
correlation = 0.9449, correlation about mean = 0.3834, overlap = 384.9
steps = 216, shift = 20, angle = 24.3 degrees
Position of cryosparc_P17_J888_009_volume_map.mrc z flip (#235) relative to
Cl3D_j591_run_it025_class002.mrc (#130) coordinates:
Matrix rotation and translation
-0.97670485 -0.09877980 -0.19049983 628.35061820
-0.19630370 0.76986862 0.60726203 -34.18266636
0.08667462 0.63051159 -0.77132526 290.90888037
Axis 0.07887912 -0.94037367 -0.33087073
Axis point 301.47094386 0.00000000 176.26702948
Rotation angle (degrees) 171.52518698
Shift along axis -14.54501139
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!98 models
> show #!99 models
> show #!219 models
> hide #!219 models
> volume flip #219
Opened cryosparc_P17_J884_009_volume_map.mrc z flip as #236, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> select add #236
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.14,0.86518,0.48153,-32.729,-0.98201,-0.059076,-0.17936,602.39,-0.12673,-0.49797,0.85788,204
> view matrix models
> #236,-0.95021,0.22201,0.21868,433.84,-0.29489,-0.86749,-0.40063,679.42,0.10076,-0.44517,0.88976,117.62
> ui mousemode right "translate selected models"
> view matrix models
> #236,-0.95021,0.22201,0.21868,442.55,-0.29489,-0.86749,-0.40063,714.68,0.10076,-0.44517,0.88976,125.94
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.96826,0.24636,0.042262,487.62,-0.23836,-0.85916,-0.4528,710.28,-0.07524,-0.4485,0.89061,176.2
> ui mousemode right "translate selected models"
> view matrix models
> #236,-0.96826,0.24636,0.042262,471.31,-0.23836,-0.85916,-0.4528,704.57,-0.07524,-0.4485,0.89061,178.79
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> select clear
> fitmap #236 inMap #98
Fit map cryosparc_P17_J884_009_volume_map.mrc z flip in map
Cl3D_j581_run_it025_class001.mrc using 185363 points
correlation = 0.8766, correlation about mean = 0.02403, overlap = 2112
steps = 192, shift = 22.6, angle = 21.2 degrees
Position of cryosparc_P17_J884_009_volume_map.mrc z flip (#236) relative to
Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
Matrix rotation and translation
-0.84354066 0.50422936 0.18491053 314.97189258
-0.50932699 -0.64184531 -0.57325441 772.53341394
-0.17036775 -0.57774333 0.79824024 267.14568387
Axis -0.00417951 0.33079007 -0.94369511
Axis point 276.01471701 384.47498501 0.00000000
Rotation angle (degrees) 147.51935105
Shift along axis 2.12587651
> hide #!98 models
> hide #!99 models
> volume flip #236
Opened cryosparc_P17_J884_009_volume_map.mrc z flip z flip as #237, grid size
294,294,294, pixel 1.9, shown at step 1, values float32
> close #236
> show #!98 models
> show #!99 models
> select add #237
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #237,0.96723,0.12731,-0.21969,22.54,0.15273,-0.9829,0.10285,476.95,-0.20284,-0.13303,-0.97013,678.92
> view matrix models
> #237,0.98911,0.12697,-0.074375,-26.233,0.1345,-0.98512,0.10698,481.46,-0.059685,-0.11582,-0.99148,640.32
> view matrix models
> #237,0.99344,0.076053,-0.08539,-10.83,0.10378,-0.91318,0.39411,386.84,-0.048004,-0.40039,-0.91509,689.4
> ui mousemode right "translate selected models"
> view matrix models
> #237,0.99344,0.076053,-0.08539,-17.742,0.10378,-0.91318,0.39411,419.91,-0.048004,-0.40039,-0.91509,662.61
> view matrix models
> #237,0.99344,0.076053,-0.08539,-17.954,0.10378,-0.91318,0.39411,412.57,-0.048004,-0.40039,-0.91509,657.54
> ui mousemode right "rotate selected models"
> view matrix models
> #237,0.99498,0.052431,-0.085289,-12.206,0.089013,-0.85322,0.5139,365.78,-0.045827,-0.51891,-0.8536,670.02
> ui mousemode right "translate selected models"
> view matrix models
> #237,0.99498,0.052431,-0.085289,4.4691,0.089013,-0.85322,0.5139,363.94,-0.045827,-0.51891,-0.8536,680.57
> select subtract #237
Nothing selected
> fitmap #237 inMap #98
Fit map cryosparc_P17_J884_009_volume_map.mrc z flip z flip in map
Cl3D_j581_run_it025_class001.mrc using 185363 points
correlation = 0.9464, correlation about mean = 0.3043, overlap = 2607
steps = 148, shift = 5.24, angle = 12.2 degrees
Position of cryosparc_P17_J884_009_volume_map.mrc z flip z flip (#237)
relative to Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
Matrix rotation and translation
0.95506772 0.17454310 -0.23954199 25.26355402
0.28049806 -0.79336127 0.54027653 283.68421592
-0.09574180 -0.58319174 -0.80667274 694.76834568
Axis -0.98759585 -0.12640897 0.09314076
Axis point 0.00000000 249.94675701 303.67322404
Rotation angle (degrees) 145.33414419
Shift along axis 3.90083895
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> volume #237 step 2
> volume #237 level 0.3935
> volume #237 level 0.3609
> volume #237 level 0.3342
> show #!98 models
> show #!97 models
> hide #!97 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!129 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!173 models
> show #!205 models
> hide #!173 models
> ui mousemode right zoom
> lighting soft
> show #!204 models
> hide #!205 models
> show #!205 models
> hide #!204 models
> show #!204 models
> show #!206 models
> hide #!205 models
> hide #!206 models
> hide #!204 models
> show #!204 models
> show #!205 models
> hide #!204 models
> hide #!205 models
> show #!234 models
> hide #!234 models
> show #!234 models
> show #!228 models
> hide #!228 models
> show #!225 models
> hide #!225 models
> show #!233 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!233 models
> hide #!232 models
> show #!225 models
> show #!233 models
> show #!234 models
> hide #!234 models
> show #!234 models
> color #233 #b2b2b2b7 models
> color #233 #b2b2b2c0 models
> color #233 #b2b2b2c6 models
> color #233 #b2b2b2ca models
> color #233 #b2b2b2cb models
> color #233 #b2b2b2cc models
> color #233 #b2b2b2ff models
> color #233 #b2b2b2f3 models
> color #233 #b2b2b2ff models
> color #233 #b2b2b2ee models
> color #233 #b2b2b2a5 models
> color #233 #b2b2b2ff models
> color #233 #b2b2b283 models
> color #233 #b2b2b298 models
> color #233 #b2b2b2ff models
[Repeated 2 time(s)]
> color #233 #b2b2b216 models
> color #233 #b2b2b22a models
> color #233 #b2b2b268 models
> color #233 #b2b2b24e models
> color #233 #b2b2b27c models
> color #233 #b2b2b236 models
> color #233 #b2b2b280 models
> color #233 #b2b2b2ff models
> hide #!233 models
> show #!233 models
> select #234/A
807 atoms, 813 bonds, 102 residues, 1 model selected
> volume flip #236sel #234/A,E
Missing or invalid "volumes" argument: only initial part "#236" of atom
specifier valid
> select #234/A,E
1615 atoms, 1626 bonds, 205 residues, 1 model selected
> color sel orange
> select #234/B,F
1320 atoms, 1326 bonds, 173 residues, 1 model selected
> color sel orange red
> select clear
> show #!233 models
> hide #!237 models
> color #233 #b2b2b272 models
> color #233 #b2b2b27c models
> show #!179 models
> hide #!179 models
> show #!178 models
> hide #!178 models
> show #!179 models
> hide #!179 models
> combine #179
No structures specified
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> select add #236
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #236,-0.012453,0.9963,-0.085041,38.532,-0.99954,-0.014744,-0.026367,562,-0.027524,0.084674,0.99603,-14.052
> view matrix models
> #236,0.059878,0.99536,-0.075321,15.571,-0.99446,0.066013,0.081795,504.47,0.086388,0.070006,0.9938,-41.09
> view matrix models
> #236,0.76783,0.50486,-0.39441,52.38,-0.29922,0.82696,0.47602,-20.228,0.56648,-0.24749,0.78603,-22.96
> lighting simple
> view matrix models
> #236,-0.88103,0.27074,-0.38793,573.03,-0.025569,0.79159,0.61052,-129.36,0.47237,0.5478,-0.69049,254.3
> view matrix models
> #236,-0.16658,-0.56618,-0.80728,733.71,-0.98446,0.049393,0.16849,478.79,-0.055524,0.8228,-0.56561,287.22
> view matrix models
> #236,0.4492,-0.45163,-0.77088,519.64,-0.80916,-0.57146,-0.13671,694.91,-0.37879,0.68517,-0.62214,432.45
> view matrix models
> #236,0.65993,-0.46974,-0.58638,407.54,-0.74905,-0.47202,-0.46488,754.94,-0.058416,0.74602,-0.66336,339.76
> view matrix models
> #236,0.53079,-0.4452,-0.72115,479.45,-0.83669,-0.41075,-0.36226,730.28,-0.13493,0.79566,-0.59052,324.57
> view matrix models
> #236,0.35401,-0.88851,0.29195,328.65,-0.68389,-0.033001,0.72884,240.28,-0.63794,-0.45768,-0.61932,813.79
> view matrix models
> #236,0.42906,-0.90235,0.040822,390.9,-0.42585,-0.16222,0.89013,152.48,-0.79659,-0.3993,-0.45387,789.83
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.42906,-0.90235,0.040822,224.14,-0.42585,-0.16222,0.89013,22.814,-0.79659,-0.3993,-0.45387,720.65
> view matrix models
> #236,0.42906,-0.90235,0.040822,264.42,-0.42585,-0.16222,0.89013,-12.91,-0.79659,-0.3993,-0.45387,709.48
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.35817,-0.93201,-0.055435,322.64,-0.41443,-0.21191,0.88507,-1.0118,-0.83664,-0.29403,-0.46215,694.69
> view matrix models
> #236,0.67931,-0.62117,-0.39075,254.89,-0.16273,-0.64672,0.74516,91.098,-0.71558,-0.44261,-0.54041,726.03
> view matrix models
> #236,0.71295,-0.55192,-0.43253,239.94,-0.10993,-0.69717,0.70842,101.7,-0.69254,-0.45753,-0.55772,729.13
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.71295,-0.55192,-0.43253,297.54,-0.10993,-0.69717,0.70842,100.6,-0.69254,-0.45753,-0.55772,732.73
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68046,-0.63817,-0.36017,307.11,0.13892,-0.37025,0.91849,-123.81,-0.7195,-0.67503,-0.16328,674.54
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68046,-0.63817,-0.36017,294.76,0.13892,-0.37025,0.91849,-125.98,-0.7195,-0.67503,-0.16328,621.96
> view matrix models
> #236,0.68046,-0.63817,-0.36017,302.19,0.13892,-0.37025,0.91849,-125.89,-0.7195,-0.67503,-0.16328,622.96
> view matrix models
> #236,0.68046,-0.63817,-0.36017,303.09,0.13892,-0.37025,0.91849,-124.21,-0.7195,-0.67503,-0.16328,623.52
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68673,-0.57216,-0.44837,311.32,0.2108,-0.43355,0.87613,-113.66,-0.69568,-0.69618,-0.17711,627
> view matrix models
> #236,0.6869,-0.56458,-0.45762,312.14,0.21863,-0.43999,0.87099,-112.46,-0.69308,-0.69833,-0.1788,627.39
> view matrix models
> #236,0.68383,-0.61388,-0.39437,306.37,0.16624,-0.39519,0.90343,-120.29,-0.71045,-0.68336,-0.16819,624.81
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68383,-0.61388,-0.39437,314.45,0.16624,-0.39519,0.90343,-114.46,-0.71045,-0.68336,-0.16819,626.72
> view matrix models
> #236,0.68383,-0.61388,-0.39437,313.59,0.16624,-0.39519,0.90343,-113.76,-0.71045,-0.68336,-0.16819,626.96
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68659,-0.57615,-0.44344,318.1,0.20666,-0.4301,0.87881,-107.76,-0.69705,-0.69503,-0.17624,628.94
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68659,-0.57615,-0.44344,327.07,0.20666,-0.4301,0.87881,-108.47,-0.69705,-0.69503,-0.17624,628.68
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.63818,-0.60887,-0.47118,358.2,0.24341,-0.42105,0.87377,-119.57,-0.7304,-0.67231,-0.1205,614.18
> view matrix models
> #236,0.63577,-0.5548,-0.53665,364.9,0.29495,-0.46787,0.83313,-108.37,-0.7133,-0.68796,-0.13382,617.88
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.63577,-0.5548,-0.53665,372.36,0.29495,-0.46787,0.83313,-107.39,-0.7133,-0.68796,-0.13382,618.18
> hide #!234 models
> hide #!233 models
> show #!233 models
> color #233 #b2b2b2ff models
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> volume #236 step 1
> volume #236 level 0.1732
> volume #236 color #009193
[Repeated 1 time(s)]
> select add #236
2 models selected
> view matrix models
> #236,0.63577,-0.5548,-0.53665,371.67,0.29495,-0.46787,0.83313,-109.23,-0.7133,-0.68796,-0.13382,606.22
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.64925,-0.56021,-0.51443,362.37,0.19972,-0.52706,0.82603,-64.458,-0.73388,-0.63904,-0.23031,629.16
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.64925,-0.56021,-0.51443,360.82,0.19972,-0.52706,0.82603,-64.722,-0.73388,-0.63904,-0.23031,636.2
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.65709,-0.56493,-0.49909,355.08,0.13448,-0.56361,0.81502,-33.193,-0.74172,-0.60266,-0.29436,648.75
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.65709,-0.56493,-0.49909,353.84,0.13448,-0.56361,0.81502,-29.68,-0.74172,-0.60266,-0.29436,652.83
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> select add #236
2 models selected
> view matrix models
> #236,0.66843,-0.53922,-0.5123,347.9,0.2468,-0.48895,0.83667,-87.981,-0.70163,-0.68569,-0.19375,632.36
> select subtract #236
Nothing selected
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> select add #236
2 models selected
> view matrix models
> #236,0.6648,-0.54898,-0.50663,349.76,0.17003,-0.54919,0.81822,-44.49,-0.72742,-0.63009,-0.27176,649.12
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.6648,-0.54898,-0.50663,348.92,0.17003,-0.54919,0.81822,-46.742,-0.72742,-0.63009,-0.27176,656.36
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.66754,-0.54182,-0.5107,347.51,0.22647,-0.50565,0.83248,-78.738,-0.70929,-0.67138,-0.21483,644.51
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.66754,-0.54182,-0.5107,347.63,0.22647,-0.50565,0.83248,-82.762,-0.70929,-0.67138,-0.21483,639.69
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.67038,-0.53268,-0.51657,346.22,0.29731,-0.44502,0.84473,-122.74,-0.67985,-0.71987,-0.13996,620.98
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.67038,-0.53268,-0.51657,347.56,0.29731,-0.44502,0.84473,-116.97,-0.67985,-0.71987,-0.13996,611.3
> select subtract #236
Nothing selected
> select add #236
2 models selected
> view matrix models
> #236,0.67038,-0.53268,-0.51657,347.92,0.29731,-0.44502,0.84473,-119.74,-0.67985,-0.71987,-0.13996,610.38
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> select add #236
2 models selected
> view matrix models
> #236,0.67038,-0.53268,-0.51657,348.46,0.29731,-0.44502,0.84473,-117.4,-0.67985,-0.71987,-0.13996,603.72
> select subtract #236
Nothing selected
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> ui mousemode right "rotate selected models"
> select add #236
2 models selected
> view matrix models
> #236,0.66305,-0.53587,-0.5227,353.3,0.32847,-0.41917,0.84641,-133.6,-0.67266,-0.7329,-0.10191,593.24
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.66305,-0.53587,-0.5227,353.67,0.32847,-0.41917,0.84641,-133.02,-0.67266,-0.7329,-0.10191,590.06
> ui mousemode right "rotate selected models"
> view matrix models
> #236,0.68404,-0.53709,-0.49359,338.97,0.31215,-0.39604,0.86355,-140.12,-0.65928,-0.74477,-0.10325,589.96
> view matrix models
> #236,0.68758,-0.51714,-0.50971,337.68,0.32634,-0.40699,0.85315,-137.85,-0.64864,-0.75294,-0.11107,591.67
> view matrix models
> #236,0.68393,-0.51897,-0.51275,340.15,0.34156,-0.39327,0.85363,-145.94,-0.64466,-0.75895,-0.091709,586.07
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> show #!235 models
> hide #!235 models
> ui tool show Matchmaker
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!234 models
> select #234/C,G
1691 atoms, 1700 bonds, 2 pseudobonds, 231 residues, 2 models selected
> color (#!234 & sel) light gray
> select clear
> select #234/D,H
1488 atoms, 1494 bonds, 1 pseudobond, 203 residues, 2 models selected
> color (#!234 & sel) dim gray
> select clear
> show #!236 models
> hide #!236 models
> show #!233 models
> hide #!233 models
> show #!235 models
> hide #!235 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> color #233 #b2b2b2cb models
> color #233 #b2b2b2be models
> color #233 #b2b2b2c0 models
> color #233 #b2b2b2bf models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
[Repeated 6 time(s)]
> color #233 #b2b2b2ed models
> color #233 #b2b2b2ff models
> lighting soft
> show #!236 models
> select add #236
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #236,0.68393,-0.51897,-0.51275,340.34,0.34156,-0.39327,0.85363,-144.79,-0.64466,-0.75895,-0.091709,589.32
> select subtract #236
Nothing selected
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> ui mousemode right zoom
> hide #!233 models
> hide #!236 models
> show #!98 models
> show #!99 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> hide #!99 models
> hide #!129 models
> hide #!130 models
> show #!98 models
> show #!99 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> hide #!98 models
> hide #!99 models
> show #!173 models
> volume flip #173
Opened cryosparc_P17_J858_007_volume_map.mrc z flip as #238, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map.mrc
Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
pixel 0.95, shown at level 0.153, step 4, values float32
> volume #239 step 1
> show #!173 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> hide #!173 models
> show #!173 models
> hide #!173 models
> show #!173 models
> hide #!173 models
> show #!173 models
> hide #!173 models
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #240, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!240 models
> show #!240 models
> show #!239 models
> hide #!239 models
> hide #!240 models
> show #!240 models
> close #238
> volume #240 level 0.1562
> hide #!240 models
> show #!240 models
> select add #240
2 models selected
> select subtract #240
Nothing selected
> view #240 clip false
No displayed objects specified.
> show #!237 models
> hide #!237 models
> close #237
> hide #!240 models
> show #!240 models
> close #240
> show #!239 models
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #237, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!237 models
> show #!237 models
> show #!233 models
> hide #!233 models
> hide #!237 models
> show #!237 models
> close #237
> show #!233 models
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc
> models #233
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!235 models
> show #!236 models
> show #!234 models
> hide #!234 models
> show #!233 models
> hide #!233 models
> hide #!235 models
> hide #!236 models
> show #!235 models
> hide #!235 models
> show #!235 models
> close #235
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!235 models
> show #!235 models
> close #235
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
\u2014\u2014\u2014 End of log from Thu Jul 18 17:16:17 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!236 models
> hide #!236 models
> show #!233 models
> show #!236 models
> hide #!236 models
> hide #!233 models
> show #!239 models
> lighting simple
> volume flip #239
Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> save
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
> models #235
> save
> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
[Repeated 1 time(s)]
\u2014\u2014\u2014 End of log from Thu Jul 18 19:11:33 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!236 models
> hide #!236 models
> hide #!235 models
> show #!236 models
> show #!233 models
> hide #!236 models
> hide #!233 models
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_0.pdb
Chain information for ranked_0.pdb #237
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_1.pdb
Chain information for ranked_1.pdb #238
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_2.pdb
Chain information for ranked_2.pdb #240
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_3.pdb
Chain information for ranked_3.pdb #241
---
Chain | Description
A | No description available
B C D | No description available
> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_4.pdb
Chain information for ranked_4.pdb #242
---
Chain | Description
A | No description available
B C D | No description available
> hide #237 models
> show #237 models
> view #237 clip false
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!235 models
> hide #!235 models
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> cofr sel
> select subtract #237
Nothing selected
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> select subtract #237
Nothing selected
> hide #238 models
> hide #240 models
> hide #241 models
> hide #242 models
> show #238 models
> hide #238 models
> show #238 models
> hide #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #240 models
> ui tool show Matchmaker
> hide #240 models
> show #237 models
> hide #237 models
> show #!211 models
> select add #211
2 models selected
> cofr sel
> view sel
> select subtract #211
Nothing selected
> show #!221 models
> hide #!221 models
> show #!177 models
> hide #!177 models
> show #!191 models
> hide #!211 models
> show #!211 models
> hide #!211 models
> show #!211 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> show #!197 models
> hide #!197 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!198 models
> hide #!191 models
> show #!191 models
> select add #191
2 models selected
> select subtract #191
Nothing selected
> select add #211
2 models selected
Drag select of 211 cryosparc_P17_J843_008_volume_map_sharp.mrc
> ui mousemode right "translate selected models"
> select #211
2 models selected
> view matrix models #211,1,0,0,23.591,0,1,0,56.577,0,0,1,-51.52
> view matrix models #211,1,0,0,22.768,0,1,0,47.717,0,0,1,-59.573
> ui tool show "Fit in Map"
> fitmap #211 inMap #191
Fit map cryosparc_P17_J843_008_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map_sharp.mrc using 95383 points
correlation = 0.8844, correlation about mean = 0.6114, overlap = 1.144e+05
steps = 204, shift = 6.18, angle = 0.216 degrees
Position of cryosparc_P17_J843_008_volume_map_sharp.mrc (#211) relative to
cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
Matrix rotation and translation
0.99999559 -0.00221335 -0.00198223 26.85415332
0.00221794 0.99999485 0.00231772 45.03607037
0.00197709 -0.00232210 0.99999535 -64.65124874
Axis -0.61542026 -0.52516117 0.58776156
Axis point 0.00000000 -8050.27859560 -1735.24699520
Rotation angle (degrees) 0.21598457
Shift along axis -78.17730413
> select subtract #211
Nothing selected
> hide #!191 models
> show #!191 models
> ui mousemode right zoom
[Repeated 1 time(s)]
> lighting soft
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!191 models
> show #!198 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> hide #!198 models
> hide #!211 models
> show #!190 models
> show #!226 models
> hide #!226 models
> show #!226 models
> color #226 #9437ffff models
> lighting simple
> hide #!190 models
> show #!190 models
> select add #226
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #226,-0.69587,-0.71701,-0.040702,705.69,-0.14519,0.19596,-0.9698,554.35,0.70334,-0.66895,-0.24047,350.03
> view matrix models
> #226,-0.55466,-0.80613,-0.20617,738.49,-0.80542,0.58236,-0.11025,383.62,0.20894,0.1049,-0.97229,500.26
> view matrix models
> #226,-0.93544,-0.34201,0.089373,633.42,-0.33939,0.93964,0.043527,102.84,-0.098865,0.010385,-0.99505,623.13
> ui mousemode right "translate selected models"
> view matrix models
> #226,-0.93544,-0.34201,0.089373,607.14,-0.33939,0.93964,0.043527,107.99,-0.098865,0.010385,-0.99505,615.3
> view matrix models
> #226,-0.93544,-0.34201,0.089373,604.94,-0.33939,0.93964,0.043527,90.344,-0.098865,0.010385,-0.99505,582.38
> ui mousemode right "rotate selected models"
> view matrix models
> #226,-0.92949,-0.35318,0.10634,601.2,-0.35497,0.93487,0.0022278,108.57,-0.1002,-0.035677,-0.99433,595.25
> ui mousemode right "translate selected models"
> view matrix models
> #226,-0.92949,-0.35318,0.10634,600.67,-0.35497,0.93487,0.0022278,112.16,-0.1002,-0.035677,-0.99433,599.08
> view matrix models
> #226,-0.92949,-0.35318,0.10634,604.71,-0.35497,0.93487,0.0022278,115.64,-0.1002,-0.035677,-0.99433,597.23
> fitmap #226 inMap #190
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 488089 points
correlation = 0.9693, correlation about mean = 0.8115, overlap = 1.318e+05
steps = 208, shift = 8.45, angle = 11.9 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#226) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97649779 -0.20178090 0.07573987 585.60429131
-0.21091477 0.96696460 -0.14315876 117.19127531
-0.04435107 -0.15576887 -0.98679737 611.32765515
Axis -0.10413305 0.99169911 -0.07542663
Axis point 308.30518170 0.00000000 301.15926555
Rotation angle (degrees) 176.52872801
Shift along axis 9.12733602
> select subtract #226
Nothing selected
> hide #!190 models
> show #!191 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> show #!190 models
> hide #!226 models
> show #!230 models
> show #!231 models
> select add #230
2 models selected
> select add #231
4 models selected
> view matrix models
> #230,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596,#231,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69,#231,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1,#231,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62,#231,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24,#231,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06,#231,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44,#231,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44
> view matrix models
> #230,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44,#231,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44
> ui mousemode right "rotate selected models"
> view matrix models
> #230,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1,#231,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1
> view matrix models
> #230,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31,#231,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31
> ui mousemode right "translate selected models"
> view matrix models
> #230,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01,#231,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01
> fitmap #230 inMap #190
Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 572767 points
correlation = 0.9702, correlation about mean = 0.8247, overlap = 1.352e+05
steps = 108, shift = 7.64, angle = 5.67 degrees
Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#230) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97635603 -0.20284331 0.07472287 586.20276261
-0.21174871 0.96698095 -0.14181092 117.11563644
-0.04349020 -0.15428042 -0.98706949 610.85909501
Axis -0.10460810 0.99170348 -0.07470851
Axis point 308.47483717 0.00000000 301.01098483
Rotation angle (degrees) 176.58308850
Shift along axis 9.18605482
> fitmap #231 inMap #190
Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
cryosparc_P17_J803_005_volume_map.mrc using 570393 points
correlation = 0.9715, correlation about mean = 0.8289, overlap = 1.331e+05
steps = 120, shift = 7.62, angle = 5.66 degrees
Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) relative to
cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
Matrix rotation and translation
-0.97634464 -0.20282850 0.07491170 586.12671435
-0.21175571 0.96700450 -0.14163978 117.05949264
-0.04371137 -0.15415222 -0.98707974 610.90239310
Axis -0.10460616 0.99170937 -0.07463300
Axis point 308.46618437 0.00000000 300.99661437
Rotation angle (degrees) 176.57124371
Shift along axis 9.18305466
> select subtract #231
2 models selected
> select subtract #230
Nothing selected
> hide #!231 models
> show #!231 models
> hide #!231 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!177 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> view matrix models #177,1,0,0,79.796,0,1,0,51.72,0,0,1,-8.0933
> ui mousemode right "rotate selected models"
> view matrix models
> #177,0.69184,0.051639,0.7202,1.2453,0.39268,0.81013,-0.4353,88.033,-0.60594,0.58396,0.54021,85.465
> view matrix models
> #177,0.68848,0.040322,0.72414,3.3706,0.40239,0.80944,-0.42765,84.826,-0.60339,0.58581,0.54106,84.445
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.68848,0.040322,0.72414,-24.721,0.40239,0.80944,-0.42765,124.91,-0.60339,0.58581,0.54106,181.95
> fitmap #177 inMap #190
Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map.mrc (#190)
using 118220 atoms
average map value = 0.2974, steps = 296
shifted from previous position = 36.4
rotated from previous position = 17.9 degrees
atoms outside contour = 74597, contour level = 0.30132
Position of 6skl (#177) relative to cryosparc_P17_J803_005_volume_map.mrc
(#190) coordinates:
Matrix rotation and translation
0.46579535 -0.09937691 0.87929456 48.24974596
0.51662113 0.83728469 -0.17904461 61.91426409
-0.71842697 0.53766029 0.44134352 233.27290342
Axis 0.38609415 0.86070423 0.33184263
Axis point 168.02643327 0.00000000 112.77870008
Rotation angle (degrees) 68.14791182
Shift along axis 149.32870821
> select subtract #177
Nothing selected
> ui mousemode right zoom
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> hide (#!177 & sel) target a
> cartoon (#!177 & sel)
> select subtract #177
Nothing selected
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!191 models
> hide #!177 models
> show #!177 models
> fitmap #177 inMap #191
Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map_sharp.mrc
(#191) using 118220 atoms
average map value = 0.3767, steps = 56
shifted from previous position = 0.0922
rotated from previous position = 0.0581 degrees
atoms outside contour = 80226, contour level = 0.39
Position of 6skl (#177) relative to
cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
Matrix rotation and translation
0.46578087 -0.09837126 0.87941531 48.10212088
0.51628561 0.83733279 -0.17978591 62.07532586
-0.71867751 0.53777030 0.44080126 233.33404225
Axis 0.38651030 0.86080969 0.33108377
Axis point 168.00088480 0.00000000 112.96763857
Rotation angle (degrees) 68.16361025
Shift along axis 149.28012082
> hide #!177 models
> show #!177 models
> hide #!191 models
> show #!191 models
> hide #!191 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
> show #237 models
> hide #237 models
> show #237 models
> matchmaker #237/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_0.pdb, chain B (#237), sequence
alignment score = 2258
RMSD between 412 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.877)
> hide #237 models
> show #237 models
> show #238 models
> matchmaker #238/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_1.pdb, chain B (#238), sequence
alignment score = 2254.4
RMSD between 411 pruned atom pairs is 0.626 angstroms; (across all 425 pairs:
0.888)
> matchmaker #240/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain B (#240), sequence
alignment score = 2264.6
RMSD between 414 pruned atom pairs is 0.635 angstroms; (across all 425 pairs:
0.838)
> show #240 models
> hide #240 models
> hide #237 models
> hide #238 models
> show #240 models
> hide #!177 models
> matchmaker #240/C to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain C (#240), sequence
alignment score = 2261.6
RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 425 pairs:
0.840)
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #240 models
> show #241 models
> matchmaker #242/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_4.pdb, chain B (#242), sequence
alignment score = 2243.6
RMSD between 412 pruned atom pairs is 0.623 angstroms; (across all 425 pairs:
0.828)
> show #242 models
> matchmaker #241/B to #177/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain H (#177) with ranked_3.pdb, chain B (#241), sequence
alignment score = 2265.2
RMSD between 410 pruned atom pairs is 0.661 angstroms; (across all 425 pairs:
0.961)
> hide #242 models
> hide #241 models
> show #242 models
> hide #242 models
> show #241 models
> show #242 models
> hide #241 models
> hide #242 models
> show #237 models
> hide #!177 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!177 models
> hide #!177 models
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> select #237/B#238/B#240/B#241/B#242/B
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> ui tool show "Color Actions"
> color sel lime green
> select #237/C#238/C#240/C#241/C#242/C
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> color sel lime green
> select #237/D#238/D#240/D#241/D#242/D
36345 atoms, 36780 bonds, 2285 residues, 5 models selected
> color sel lime green
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> show #!177 models
> color sel medium blue
> color sel dark blue
> color sel medium blue
[Repeated 1 time(s)]
> color sel purple
> color sel blue
> color sel medium blue
[Repeated 1 time(s)]
> select clear
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #!190 models
> hide #!190 models
> show #238 models
> hide #238 models
> show #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #238 models
> show #238 models
> hide #238 models
> show #238 models
> hide #238 models
> hide #237 models
> show #240 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #240 models
> show #240 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #240 models
> show #241 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> show #242 models
> hide #242 models
> show #242 models
> hide #241 models
> show #241 models
> hide #241 models
> show #241 models
> hide #242 models
> show #237 models
> hide #237 models
> show #237 models
> hide #241 models
> show #241 models
> hide #241 models
> show #241 models
> hide #237 models
> hide #241 models
> show #237 models
> hide #237 models
> show #238 models
> show #237 models
> hide #238 models
> show #238 models
> hide #237 models
> hide #238 models
> show #240 models
> show #237 models
> hide #237 models
> hide #240 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #!239 models
> hide #!239 models
> show #240 models
> hide #240 models
> show #237 models
> hide #237 models
> show #238 models
> hide #238 models
> show #237 models
> ui tool show "Show Sequence Viewer"
> sequence chain #237/A
Alignment identifier is 237/A
> select #237/A:746
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #237/A:746-757
193 atoms, 193 bonds, 12 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 193 atom styles
> style sel sphere
Changed 193 atom styles
> style sel ball
Changed 193 atom styles
> select ~sel & ##selected
38920 atoms, 39296 bonds, 2455 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> select #237/A#238/A#240/A#241/A#242/A
86530 atoms, 87105 bonds, 5480 residues, 5 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel royal blue
> select clear
> show #238 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #238 models
> show #240 models
> show #237 models
> hide #240 models
> show #240 models
> hide #240 models
> show #240 models
> hide #240 models
> hide #!177 models
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> select subtract #237
Nothing selected
> select add #237
39113 atoms, 39489 bonds, 2467 residues, 1 model selected
> show sel target ab
> hide sel target a
> cartoon sel
> ui tool show "Show Sequence Viewer"
> sequence chain #237/A
Alignment identifier is 237/A
> select subtract #237
Nothing selected
> select #237/A:746-747
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #237/A:746-757
193 atoms, 193 bonds, 12 residues, 1 model selected
> select #237/A:744
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #237/A:744-759
254 atoms, 255 bonds, 16 residues, 1 model selected
> show sel target ab
> combine #237
> hide #237 models
> show #237 models
> hide #243 models
> select #237/A:743
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #237/A:1-743
11627 atoms, 11702 bonds, 743 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #237/A:761
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #237/A:761-1096
5405 atoms, 5441 bonds, 336 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #237/A:744
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #237/A
274 atoms, 276 bonds, 17 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 274 atom styles
> select clear
> show #!211 models
> lighting soft
> color #211 #ffffb27e models
> color #211 #ffffb2c3 models
> color #211 #ffffb2ad models
> color #211 #ffffb29d models
> color #211 #ffffb28e models
> color #211 #ffffb28f models
> lighting full
> lighting simple
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes true
> color #211 #ffffb2b0 models
> color #211 #ffffb2d5 models
> color #211 #ffffb2ec models
> color #211 #ffffb2ca models
> color #211 #ffffb227 models
> color #211 #ffffb290 models
> color #211 #ffffb2b1 models
> color #211 #ffffb282 models
> color #211 #ffffb2ff models
> lighting soft
> volume #211 level 0.6913
> volume #211 level 0.65
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> show #!231 models
> hide #!230 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> color #231 #b2ffb2d9 models
> color #231 #b2ffb2c1 models
> color #231 #b2ffb2a3 models
> color #231 #b2ffb27f models
> color #231 #b2ffb26e models
> color #231 #b2ffb2ff models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!231 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> set bgColor black
> set bgColor transparent
> ui tool show "Fit in Map"
> show #243 models
> hide #243 models
> show #237 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!231 models
> show #!231 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #237 inMap #231
Fit molecule ranked_0.pdb (#237) to map
cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) using 22081 atoms
average map value = 0.3487, steps = 116
shifted from previous position = 1.47
rotated from previous position = 1.84 degrees
atoms outside contour = 10270, contour level = 0.3
Position of ranked_0.pdb (#237) relative to
cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) coordinates:
Matrix rotation and translation
0.07105997 -0.95640246 -0.28327514 285.99602561
0.71998545 0.24572901 -0.64902865 297.83602531
0.69034152 -0.15783402 0.70605736 373.36846355
Axis 0.24561334 -0.48684010 0.83824865
Axis point -161.36898166 394.59093851 0.00000000
Rotation angle (degrees) 89.34548655
Shift along axis 238.22153124
> hide #237 models
> show #237 models
> color #231 #b2ffb283 models
> set bgColor white
> set bgColor #ffffff00
> color #231 #b2ffb282 models
> color #231 #b2ffb292 models
> color #231 #b2ffb2ae models
> color #231 #b2ffb2bd models
> color #231 #b2ffb295 models
> lighting full
> lighting simple
> color #231 #b2ffb2ff models
> color #231 #b2ffb29d models
> color #231 #b2ffb2d4 models
> color #231 #b2ffb2af models
> color #231 #b2ffb2ff models
> lighting soft
> lighting full
> lighting soft
> hide #237 models
> set bgColor black
> set bgColor transparent
> hide #!231 models
> show #!230 models
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> show #!226 models
> hide #!230 models
> show #!231 models
> hide #!226 models
> hide #!231 models
> show #!211 models
> show #!232 models
> hide #!232 models
> hide #!211 models
> show #!235 models
> hide #!235 models
> show #!233 models
> show #!232 models
> show #!236 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!232 models
> show #!232 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!236 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!236 models
> hide #!232 models
> hide #!233 models
> show #!233 models
> hide #!236 models
> select add #233
2 models selected
> cofr sel
> select subtract #233
Nothing selected
> show #!236 models
> show #!232 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!231 models
> hide #!231 models
> show #!230 models
> hide #!230 models
> show #!231 models
> hide #!231 models
> hide #!236 models
> show #!236 models
> show #!234 models
> hide #!234 models
> hide #!236 models
> color #233 #b2b2b2b0 models
> hide #!233 models
> hide #!232 models
> show #!191 models
> hide #!191 models
> show #!211 models
> hide #!211 models
> show #!231 models
> show #!177 models
> hide #!177 models
> show #237 models
> hide #237 models
> hide #!231 models
> show #!233 models
> color #233 #b2b2b2ff models
> show #!236 models
> hide #!236 models
> show #!236 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Refine3D/job814/run_class001.mrc
Opened run_class001.mrc as #244, grid size 588,588,588, pixel 0.95, shown at
level 0.00486, step 4, values float32
> close #244
> hide #!236 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> lighting full
> show #!236 models
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> hide #!236 models
> show #!236 models
> hide #!233 models
> show #!233 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
\u2014\u2014\u2014 End of log from Wed Jul 24 16:21:27 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!236 models
> hide #!233 models
> show #!98 models
> lighting simple
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!100 models
> hide #!100 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!99 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!99 models
> show #!99 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!99 models
> show #!32 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!34 models
> show #!129 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!129 models
> hide #!130 models
> show #!74 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!74 models
> show #!75 models
> hide #!75 models
> hide #!74 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!122 models
> show #!129 models
> hide #!122 models
> show #!122 models
> hide #!129 models
> show #!129 models
> hide #!129 models
> show #!129 models
> hide #!122 models
> show #!122 models
> hide #!129 models
> show #!123 models
> hide #!122 models
> hide #!123 models
> show #!123 models
> show #!124 models
> hide #!124 models
> show #!122 models
> hide #!122 models
> show #!130 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> hide #!123 models
> show #!123 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!110 models
> show #!110 models
> hide #!123 models
> show #!123 models
> hide #!110 models
> show #!110 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!123 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> show #!32 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!112 models
> hide #!112 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!110 models
> hide #!111 models
> hide #!32 models
> hide #!34 models
> show #!123 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!129 models
> hide #!129 models
> show #!130 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!75 models
> show #!75 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> hide #!74 models
> show #!74 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!122 models
> show #!122 models
> hide #!123 models
> show #!123 models
> hide #!122 models
> hide #!74 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!123 models
> show #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!123 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!130 models
> show #!130 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> show #!75 models
> hide #!75 models
> hide #!130 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
pixel 1.9, shown at level 0.37, step 2, values float32
> lighting simple
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #244 step 1
> volume #244 level 0.344
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J685_007_volume_map.mrc
Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
pixel 1.9, shown at level 0.361, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J690_006_volume_map.mrc
Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
pixel 1.9, shown at level 0.36, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #245 step 1
> volume #245 level 0.3413
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #246 step 1
> show #!245 models
> hide #!245 models
> show #!245 models
> select add #245
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.24392,0.87788,0.4121,-128.61,0.92708,-0.086349,-0.36479,125.94,-0.28466,0.47103,-0.83493,401.32
> view matrix models
> #245,0.64106,-0.054068,-0.76558,302.83,0.031113,-0.99486,0.096313,510.77,-0.76686,-0.085561,-0.63609,638.94
> view matrix models
> #245,0.9162,-0.026949,-0.39982,128.81,0.14241,-0.91071,0.38773,385.27,-0.37456,-0.41217,-0.83055,665.84
> view matrix models
> #245,0.91682,-0.37423,-0.13924,159.29,-0.35009,-0.92108,0.17043,579.11,-0.19203,-0.1075,-0.97548,567.39
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.91682,-0.37423,-0.13924,163.24,-0.35009,-0.92108,0.17043,567.35,-0.19203,-0.1075,-0.97548,639.7
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.98493,-0.05987,-0.16227,64.254,-0.032068,-0.98512,0.16883,496.24,-0.16996,-0.16108,-0.9722,647.31
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.98493,-0.05987,-0.16227,72.788,-0.032068,-0.98512,0.16883,503.81,-0.16996,-0.16108,-0.9722,638.94
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.96022,0.026881,-0.27794,84.445,0.064645,-0.98972,0.12761,488.12,-0.27165,-0.1405,-0.95208,656.85
> ui mousemode right "rotate selected models"
> view matrix models
> #245,0.96845,0.06341,-0.24101,63.142,0.079191,-0.99527,0.056358,503.03,-0.23629,-0.073665,-0.96889,632.88
> ui mousemode right "translate selected models"
> view matrix models
> #245,0.96845,0.06341,-0.24101,55.646,0.079191,-0.99527,0.056358,515.43,-0.23629,-0.073665,-0.96889,633.64
> select subtract #245
Nothing selected
> hide #!245 models
> show #!246 models
> select add #246
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #246,-0.94249,-0.14738,0.29999,492.53,0.01794,-0.91854,-0.39491,640.24,0.33376,-0.36682,0.86836,47.073
> view matrix models
> #246,-0.98683,-0.012271,0.16129,511.21,-0.0067172,-0.99315,-0.11666,581.14,0.16162,-0.11621,0.97999,-7.5123
> view matrix models
> #246,-0.99462,-0.028395,0.099663,536.91,0.012491,-0.98757,-0.15671,586.65,0.10287,-0.15462,0.9826,18.639
> select subtract #246
Nothing selected
> select add #246
2 models selected
> select subtract #246
Nothing selected
> show #!245 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #245 inMap #244
Fit map cryosparc_P17_J685_007_volume_map.mrc in map
cryosparc_P17_J368_007_volume_map.mrc using 271515 points
correlation = 0.9949, correlation about mean = 0.9457, overlap = 9.464e+04
steps = 188, shift = 2.56, angle = 15.2 degrees
Position of cryosparc_P17_J685_007_volume_map.mrc (#245) relative to
cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
Matrix rotation and translation
0.99981329 -0.01923951 0.00179460 4.69427957
-0.01931352 -0.99208863 0.12404490 525.91853508
-0.00060616 -0.12405640 -0.99227498 588.72614471
Axis -0.99995314 0.00967608 -0.00029828
Axis point 0.00000000 281.31245766 277.98752927
Rotation angle (degrees) 172.87372921
Shift along axis 0.21916772
> fitmap #246 inMap #244
Fit map cryosparc_P17_J690_006_volume_map.mrc in map
cryosparc_P17_J368_007_volume_map.mrc using 254434 points
correlation = 0.9952, correlation about mean = 0.9446, overlap = 9.256e+04
steps = 120, shift = 8.54, angle = 6.45 degrees
Position of cryosparc_P17_J690_006_volume_map.mrc (#246) relative to
cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
Matrix rotation and translation
-0.99997157 0.00691924 -0.00299642 557.81739805
-0.00648161 -0.99184550 -0.12728119 593.36152310
-0.00385267 -0.12725815 0.99186215 38.74337635
Axis 0.00171577 0.06376541 -0.99796344
Axis point 279.94000643 296.98029450 0.00000000
Rotation angle (degrees) 179.61530751
Shift along axis 0.12855455
> hide #!246 models
> hide #!244 models
> show #!246 models
> ui mousemode right zoom
> lighting soft
> hide #!245 models
> show #!245 models
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!245 models
> show #!245 models
> hide #!246 models
> hide #!245 models
> show #!244 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!244 models
> hide #!244 models
> show #!244 models
> volume #244 level 0.36
> hide #!246 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!244 models
> hide #!244 models
> show #!244 models
> hide #!246 models
> show #!246 models
> hide #!244 models
> show #!245 models
> show #!244 models
> hide #!246 models
> hide #!245 models
> show #!245 models
> volume #245 level 0.36
> hide #!244 models
> show #!246 models
> hide #!246 models
> show #!246 models
> hide #!245 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J697_006_volume_map.mrc
Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J712_007_volume_map.mrc
Opened cryosparc_P17_J712_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.349, step 2, values float32
> hide #!246 models
> show #!246 models
> hide #!246 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #247 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #248 step 1
> volume #247 level 0.36
> volume #248 level 0.36
> close #248
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J362_007_volume_map.mrc
Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
pixel 1.9, shown at level 0.368, step 2, values float32
> hide #!247 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #248 step 1
> volume #248 level 0.36
> show #!244 models
> hide #!248 models
> show #!248 models
> hide #!244 models
> show #!244 models
> hide #!248 models
> show #!248 models
> hide #!244 models
> hide #!248 models
> show #!248 models
> show #!246 models
> show #!247 models
> hide #!247 models
> hide #!248 models
> show #!248 models
> hide #!248 models
> show #!248 models
> hide #!246 models
> show #!246 models
> hide #!248 models
> hide #!246 models
> show #!98 models
> show #!110 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!34 models
> hide #!32 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> show #!99 models
> hide #!110 models
> show #!111 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!219 models
> show #!220 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!99 models
> show #!99 models
> hide #!99 models
> hide #!34 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #219 step 1
> volume #220 level 0.35
> volume #219 level 0.35
> volume #219 step 2
> volume #219 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #220 step 2
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1103_006_volume_map.mrc
Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
pixel 1.9, shown at level 0.358, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1105_008_volume_map.mrc
Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
pixel 1.9, shown at level 0.362, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1106_006_volume_map.mrc
Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
pixel 1.9, shown at level 0.357, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1107_006_volume_map.mrc
Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
pixel 1.9, shown at level 0.356, step 2, values float32
> hide #!219 models
> hide #!220 models
> hide #!249 models
> hide #!250 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #251 step 1
> volume #251 level 0.3333
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #252 step 1
> volume #252 level 0.33
> volume #252 level 0.35
> volume #252 level 0.34
> hide #!252 models
> show #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> show #!32 models
> hide #!34 models
> show #!34 models
> hide #!32 models
> hide #!34 models
> show #!98 models
> show #!99 models
> hide #!99 models
> hide #!98 models
> show #!99 models
> show #!98 models
> hide #!99 models
> hide #!98 models
> show #!99 models
> hide #!99 models
> show #!110 models
> show #!111 models
> hide #!110 models
> show #!110 models
> hide #!111 models
> show #!111 models
> hide #!111 models
> hide #!110 models
> show #!246 models
> hide #!246 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
\u2014\u2014\u2014 End of log from Tue Jul 30 11:34:25 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!232 models
> hide #!232 models
> show #!234 models
> show #!236 models
> lighting simple
> close #1-18
> close #22-27,32-75
> close #98-135
> close #85-90
> show #!244 models
> hide #!244 models
> close #244-252
> show #!19 models
> hide #!19 models
> open 8XGC fromDatabase pdb format mmcif
8xgc title:
Structure of yeast replisome associated with FACT and histone hexamer,
Composite map [more info...]
Chain information for 8xgc #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
8 | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
9 | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
M | FACT complex subunit POB3 | POB3_YEAST 1-552
N R | Histone H3 | A0A6A5Q536_YEASX 1-136
O S | Histone H4 | H4_YEAST 1-103
P | Histone H2A.1 | H2A1_YEAST 1-132
Q | Histone H2B.2 | H2B2_YEAST 1-131
X | DNA (51-MER) |
Y | DNA (39-MER) |
Non-standard residues in 8xgc #1
---
ADP \u2014 adenosine-5'-diphosphate
ZN \u2014 zinc ion
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,47.645,0,1,0,-186.91,0,0,1,-225.38
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.58597,0.26748,0.76491,-77.764,-0.68071,0.6746,0.28556,-31.019,-0.43963,-0.68802,0.57737,101.42
> view matrix models
> #1,-0.63049,-0.77581,0.02448,555.31,-0.40378,0.30088,-0.86396,224.99,0.66291,-0.5546,-0.50296,59.311
> view matrix models
> #1,-0.60522,-0.79563,-0.026037,564.5,-0.4515,0.37002,-0.81194,209.77,0.65563,-0.47965,-0.58317,61.313
> view matrix models
> #1,-0.51594,-0.8087,-0.28251,600.78,-0.65671,0.58517,-0.47573,138.81,0.55003,-0.059923,-0.83299,45.531
> view matrix models
> #1,-0.75431,-0.62553,0.19933,513.87,-0.20404,-0.065216,-0.97679,283.54,0.62401,-0.77747,-0.078442,28.164
> view matrix models
> #1,0.75405,0.27605,-0.59599,163.26,0.6559,-0.26853,0.70547,-200.8,0.034703,-0.92287,-0.38355,247.17
> view matrix models
> #1,0.73033,0.35167,-0.58562,150.07,0.68309,-0.37214,0.62842,-168.74,0.0030683,-0.85898,-0.51201,266.6
> view matrix models
> #1,0.72602,0.36576,-0.58233,147.32,0.68766,-0.39043,0.61212,-162.48,-0.0034657,-0.84486,-0.53498,269.69
> select subtract #1
Nothing selected
> show #!177 models
> hide #!177 models
> show #!177 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.46578,-0.098371,0.87942,92.221,0.51629,0.83733,-0.17979,-43.763,-0.71868,0.53777,0.4408,171.47
> ui mousemode right "rotate selected models"
> view matrix models
> #177,-0.49891,-0.69823,-0.51339,651.92,-0.83168,0.55231,0.057061,237.03,0.24371,0.45544,-0.85626,230.01
> view matrix models
> #177,0.26698,-0.55614,-0.78704,521.35,-0.5875,0.55345,-0.59037,305.23,0.76392,0.62,-0.17897,-27.896
> ui mousemode right "translate selected models"
> view matrix models
> #177,0.26698,-0.55614,-0.78704,529.97,-0.5875,0.55345,-0.59037,261.16,0.76392,0.62,-0.17897,-91.066
> view matrix models
> #177,0.26698,-0.55614,-0.78704,447.11,-0.5875,0.55345,-0.59037,192.81,0.76392,0.62,-0.17897,-38.287
> select subtract #177
Nothing selected
> ui tool show "Fit in Map"
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> fitmap #177 inMap #236
Fit molecule 6skl (#177) to map cryosparc_P17_J544_007_volume_map_zflip.mrc
(#236) using 118220 atoms
average map value = 0.2679, steps = 436
shifted from previous position = 21.5
rotated from previous position = 40.5 degrees
atoms outside contour = 24734, contour level = 0.17324
Position of 6skl (#177) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.51563097 -0.12952906 -0.84696336 558.27691744
-0.84526058 -0.08486257 0.52757265 364.76426350
-0.14021148 0.98793753 -0.06572804 118.82779302
Axis 0.41616323 -0.63889353 -0.64701099
Axis point 390.84775709 -13.99098898 0.00000000
Rotation angle (degrees) 146.41962992
Shift along axis -77.59409021
> hide #!236 models
> show #!236 models
> hide #!236 models
> show #!236 models
> hide #!234 models
> show #!234 models
> show #!232 models
> hide #!234 models
> show #!233 models
> hide #!236 models
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #1/E to #177/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain E (#177) with 8xgc, chain E (#1), sequence alignment
score = 3091.5
RMSD between 562 pruned atom pairs is 0.577 angstroms; (across all 562 pairs:
0.577)
> hide #!233 models
> hide #!232 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> cartoon style (#!177 & sel) modeHelix tube sides 20
> select subtract #177
Nothing selected
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> matchmaker #!1 to #177
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> matchmaker #1/I to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!177 models
> show #!177 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #237 models
> hide #237 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> show #237 models
> show #!234 models
> hide #!234 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> combine #237
> hide #237 models
> show #243 models
> hide #243 models
> show #243 models
> hide #243 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> show #237 models
> hide #237 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> hide #2 models
> close #2
> open /Users/cvetkom/Documents/AlphaFold/yCsm3_Tof1_Oliver/yCsm3Tof1_AF.pdb
Chain information for yCsm3Tof1_AF.pdb #2
---
Chain | Description
A | No description available
B | No description available
> select add #2
24908 atoms, 25142 bonds, 1555 residues, 1 model selected
> view sel
> select clear
> matchmaker #2/A to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with yCsm3Tof1_AF.pdb, chain A (#2), sequence
alignment score = 5355
RMSD between 517 pruned atom pairs is 1.040 angstroms; (across all 665 pairs:
2.956)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:612
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:612-643
528 atoms, 528 bonds, 32 residues, 1 model selected
> select #2/A:612-613
35 atoms, 34 bonds, 2 residues, 1 model selected
> select #2/A:613-657
731 atoms, 731 bonds, 45 residues, 1 model selected
> color sel blue
> color sel orange red
> select clear
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #!236 models
> hide #!236 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
440,440,440, pixel 0.95, shown at level 0.0283, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_EMReady.mrc
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
440,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1207_map_sharp.mrc
Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
0.95, shown at level 2.63e-06, step 2, values float32
> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1210_map_sharp.mrc
Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
0.95, shown at level 0.000291, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
440,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1163_006_volume_map.mrc
Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
pixel 0.95, shown at level 0.155, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
588,588,588, pixel 0.95, shown at level 0.153, step 4, values float32
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #2 models
> show #!236 models
> show #!9 models
> volume #9 step 1
> select add #9
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,44.079,0,1,0,-129.91,0,0,1,33.561
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.89241,-0.2853,-0.34957,745.33,-0.22047,0.95166,-0.21387,0.58537,0.39369,-0.11379,-0.91217,447.06
> view matrix models
> #9,-0.86115,-0.40726,-0.30424,765.4,-0.37668,0.9131,-0.15612,41.487,0.34138,-0.019841,-0.93972,437.48
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.86115,-0.40726,-0.30424,699.37,-0.37668,0.9131,-0.15612,-44.304,0.34138,-0.019841,-0.93972,339.64
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.93636,-0.11772,-0.33072,631.45,-0.22073,0.93,0.2939,-206.54,0.27297,0.34819,-0.8968,226.48
> ui mousemode right zoom
> fitmap #9 inMap #236
Fit map cryosparc_P17_J864_007_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028136 points
correlation = 0.9937, correlation about mean = 0.9426, overlap = 1.458e+05
steps = 468, shift = 23.6, angle = 33.5 degrees
Position of cryosparc_P17_J864_007_volume_map_zflip.mrc (#9) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96823974 -0.24332681 -0.05747924 633.07873275
0.10233189 -0.59543288 0.79686125 204.91238326
-0.22812274 0.76567078 0.60142188 -52.82098481
Axis -0.08064861 0.44122957 0.89376298
Axis point 302.77781545 150.02897929 0.00000000
Rotation angle (degrees) 168.85032375
Shift along axis -7.85295761
> select subtract #9
Nothing selected
> show #!8 models
> volume #8 step 1
> select add #8
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83981,0.16349,-0.51768,159.04,-0.33783,0.90383,-0.26259,201.97,0.42496,0.39542,0.81428,-171.03
> view matrix models
> #8,-0.088093,0.71527,-0.69328,321.17,0.1227,0.69847,0.70504,-168.1,0.98853,-0.022959,-0.1493,82.529
> view matrix models
> #8,0.18202,-0.63889,-0.74746,635.26,0.31514,-0.68216,0.65981,172.32,-0.93143,-0.35565,0.077172,642.94
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.18202,-0.63889,-0.74746,569.25,0.31514,-0.68216,0.65981,-13.259,-0.93143,-0.35565,0.077172,525.18
> view matrix models
> #8,0.18202,-0.63889,-0.74746,562.71,0.31514,-0.68216,0.65981,-14.599,-0.93143,-0.35565,0.077172,487.95
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.49045,-0.55087,-0.67528,429.78,0.60915,-0.33743,0.71769,-209.84,-0.62321,-0.76334,0.17007,485.31
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.49045,-0.55087,-0.67528,444.24,0.60915,-0.33743,0.71769,-178.89,-0.62321,-0.76334,0.17007,497.07
> fitmap #8 inMap #236
Fit map cryosparc_P17_J1163_006_volume_map.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2031120 points
correlation = 0.9907, correlation about mean = 0.9161, overlap = 1.477e+05
steps = 368, shift = 21.9, angle = 21.5 degrees
Position of cryosparc_P17_J1163_006_volume_map.mrc (#8) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
0.99949009 -0.03184645 0.00231562 7.34723952
0.03147411 0.99482700 0.09658474 -35.10247418
-0.00537952 -0.09646261 0.99532207 32.64947374
Axis -0.94951030 0.03784884 0.31144447
Axis point 0.00000000 313.97495420 380.98360453
Rotation angle (degrees) 5.83455364
Shift along axis 1.86363064
> select add #8
4 models selected
> select subtract #8
Nothing selected
> lighting soft
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 silver models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J959_008_volume_map_zflip.mrc
Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
588,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
> select add #10
3 models selected
> view matrix models #10,1,0,0,23.505,0,1,0,-15.929,0,0,1,-23.739
> lighting simple
> view matrix models #10,1,0,0,124.8,0,1,0,-99.812,0,0,1,-122.71
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.42765,0.3857,-0.81752,672.45,0.75258,-0.34906,-0.55837,194.61,-0.50073,-0.85404,-0.141,572.88
> view matrix models
> #10,-0.5836,0.78463,0.2092,308.37,-0.51615,-0.15955,-0.84151,586.63,-0.62689,-0.59908,0.4981,352.72
> view matrix models
> #10,-0.66506,0.6951,0.273,334.38,-0.54368,-0.20005,-0.8151,596.53,-0.51196,-0.69052,0.51096,339.61
> view matrix models
> #10,-0.87025,-0.14082,0.47205,540.96,-0.24214,-0.71221,-0.65888,593.45,0.42898,-0.68769,0.58571,53.595
> view matrix models
> #10,-0.51532,-0.60142,0.61052,515.4,0.36144,-0.79846,-0.48148,393.16,0.77704,-0.027449,0.62885,-221.63
> view matrix models
> #10,-0.57269,-0.31806,0.75556,417.1,0.29571,-0.93976,-0.17146,353.87,0.76458,0.12523,0.63225,-257.33
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.57269,-0.31806,0.75556,316.03,0.29571,-0.93976,-0.17146,301.69,0.76458,0.12523,0.63225,-291.73
> view matrix models
> #10,-0.57269,-0.31806,0.75556,307.58,0.29571,-0.93976,-0.17146,309.28,0.76458,0.12523,0.63225,-267.22
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.69988,-0.20741,0.68348,337.07,0.084924,-0.97429,-0.2087,387.97,0.70919,-0.088019,0.6995,-218.61
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.69988,-0.20741,0.68348,322.79,0.084924,-0.97429,-0.2087,374.73,0.70919,-0.088019,0.6995,-205.24
> volume #10 step 1
> fitmap #10 inMap #236
Fit map cryosparc_P17_J959_008_volume_map_zflip.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028921 points
correlation = 0.9436, correlation about mean = 0.7528, overlap = 1.329e+05
steps = 224, shift = 12.9, angle = 13.2 degrees
Position of cryosparc_P17_J959_008_volume_map_zflip.mrc (#10) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96431898 -0.25440259 0.07326822 606.33395084
-0.22036646 0.61794867 -0.75470396 377.39307444
0.14672264 -0.74392121 -0.65196143 620.81486733
Axis 0.13202542 -0.89938569 0.41674293
Axis point 323.81378637 0.00000000 404.72898510
Rotation angle (degrees) 177.65962530
Shift along axis -0.65022839
> select add #10
4 models selected
> select subtract #10
Nothing selected
> color #10 #945200ff models
> color #10 #941100ff models
> color #10 #945200ff models
> color #10 #ff9300ff models
> color #10 #ff2600ff models
> color #10 #ff7e79ff models
> color #10 #fffc79ff models
> color #10 #d4fb79ff models
> color #10 #fffc79ff models
> color #10 #d4fb79ff models
> volume #10 level 0.1697
> volume #10 level 0.1731
> ui mousemode right zoom
> lighting soft
> hide #!10 models
> show #!10 models
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job802_run_class001.mrc
Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
0.95, shown at level 0.00416, step 4, values float32
> lighting simple
> select add #11
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-51.74,0,1,0,-84.314,0,0,1,-73.541
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.0036933,-0.45538,0.89029,72.314,-0.79632,0.53717,0.27807,170.48,-0.60486,-0.70998,-0.36065,684.31
> view matrix models
> #11,-0.90602,-0.026747,0.4224,361.01,-0.42311,0.032534,-0.90549,549.65,0.010478,-0.99911,-0.040793,487.81
> view matrix models
> #11,-0.90163,0.38295,-0.20102,445.5,0.0063584,-0.453,-0.89149,546.69,-0.43245,-0.80508,0.406,428.35
> view matrix models
> #11,-0.68901,-0.48447,0.53903,379.58,0.2377,-0.85366,-0.46343,452.94,0.68467,-0.19118,0.70333,-127.8
> view matrix models
> #11,-0.70406,-0.10147,0.70285,238.48,-0.37448,-0.78789,-0.48887,615.54,0.60338,-0.60739,0.51673,55.46
> view matrix models
> #11,-0.76623,0.05272,0.6404,236.16,-0.49162,-0.68984,-0.53144,636.65,0.41376,-0.72204,0.5545,125.83
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.76623,0.05272,0.6404,261.62,-0.49162,-0.68984,-0.53144,557.66,0.41376,-0.72204,0.5545,116.13
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.60221,0.45689,0.65467,110.25,-0.62773,-0.77766,-0.034707,467.75,0.49325,-0.43186,0.75511,-39.317
> view matrix models
> #11,-0.68577,0.26569,0.67759,174.57,-0.57475,-0.76886,-0.28021,524.85,0.44652,-0.58161,0.67996,33.93
> volume #11 step 1
> fitmap #11 inMap #236
Fit map Ref3D_job802_run_class001.mrc in map
cryosparc_P17_J544_007_volume_map_zflip.mrc using 2030281 points
correlation = 0.9571, correlation about mean = 0.8205, overlap = 3535
steps = 488, shift = 19.8, angle = 32.9 degrees
Position of Ref3D_job802_run_class001.mrc (#11) relative to
cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
Matrix rotation and translation
-0.96450343 -0.25313673 0.07519943 605.61171904
-0.21928378 0.60909585 -0.76217904 383.34466562
0.14713185 -0.75161431 -0.64298380 621.67767309
Axis 0.13173116 -0.89692214 0.42211086
Axis point 323.99781428 0.00000000 407.81801536
Rotation angle (degrees) 177.70184669
Shift along axis -1.63548244
> hide #!10 models
> select add #11
4 models selected
> select subtract #11
Nothing selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!233 models
> show #!3 models
> volume #3 step 1
> volume #3 level 0.2689
> hide #!3 models
> show #!3 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> fitmap #3 inMap #233
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc using 171797 points
correlation = 0.9986, correlation about mean = 0.9835, overlap = 1.873e+05
steps = 64, shift = 2.32, angle = 0.05 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc (#233) coordinates:
Matrix rotation and translation
0.99999969 -0.00055856 -0.00055446 0.28221116
0.00055877 0.99999977 0.00037517 -0.20830704
0.00055425 -0.00037548 0.99999978 -2.35151229
Axis -0.43044636 -0.63576954 0.64071291
Axis point 2074.34448759 -648.53479123 0.00000000
Rotation angle (degrees) 0.04995831
Shift along axis -1.49568576
> volume #3 level 0.25
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!234 models
> hide #!236 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!232 models
> show #!234 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> select add #234
18238 atoms, 19000 bonds, 223 pseudobonds, 1946 residues, 5 models selected
> view matrix models
> #232,-0.019001,-0.99844,0.052579,192.68,-0.84729,0.043998,0.5293,242.41,-0.53078,-0.034493,-0.84681,167.29,#234,-0.045299,-0.99887,-0.014131,189.08,-0.79838,0.027697,0.60152,244.8,-0.60045,0.03853,-0.79874,172.18
> ui mousemode right "translate selected models"
> view matrix models
> #232,-0.019001,-0.99844,0.052579,192.71,-0.84729,0.043998,0.5293,242.76,-0.53078,-0.034493,-0.84681,167.34,#234,-0.045299,-0.99887,-0.014131,189.11,-0.79838,0.027697,0.60152,245.15,-0.60045,0.03853,-0.79874,172.22
> select subtract #234
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> select subtract #232
Nothing selected
> hide #!234 models
> show #!234 models
> hide #!232 models
> hide #!234 models
> volume flip #4,5,6
Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
440,440,440, pixel 0.95, shown at step 1, values float32
Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
pixel 0.95, shown at step 1, values float32
Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
pixel 0.95, shown at step 1, values float32
> hide #!13 models
> volume #12 level 0.6868
> hide #!14 models
> volume #12 level 1.994
> volume #12 level 2.112
> hide #!12 models
> show #!13 models
> volume #13 level 0.04456
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!13 models
> show #!14 models
> volume #14 level 0.06454
> volume #14 level 0.1669
> hide #!14 models
> show #!14 models
> volume #14 level 0.2071
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!7 models
> volume #7 level 0.1489
> volume #7 step 1
> volume #7 level 0.2483
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #7
3 models selected
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95557,0.0046513,-0.29472,69.933,0.27535,0.34272,0.89818,-107.26,0.10519,-0.93943,0.32621,316.27
> view matrix models
> #7,0.91915,0.11688,-0.37617,70.997,0.39267,-0.1961,0.89853,-18.651,0.031252,-0.97359,-0.22614,454.39
> view matrix models
> #7,0.91426,0.13556,-0.38178,69.268,0.40482,-0.26848,0.87409,-0.87336,0.015992,-0.9537,-0.30034,468.92
> view matrix models
> #7,0.95579,-0.038803,-0.29149,78.32,0.26406,-0.32299,0.90882,32.378,-0.12941,-0.94561,-0.29846,496.89
> view matrix models
> #7,0.94972,0.029908,-0.31167,69.398,0.30564,-0.30453,0.90213,21.312,-0.067931,-0.95203,-0.29836,485.5
> view matrix models
> #7,0.9488,-0.094559,-0.30141,93.528,0.2555,-0.33137,0.90825,36.024,-0.18576,-0.93875,-0.29025,505.38
> view matrix models
> #7,0.95015,-0.094376,-0.29717,92.323,0.25152,-0.33129,0.90939,36.591,-0.18427,-0.9388,-0.29104,505.25
> view matrix models
> #7,0.95804,-0.094732,-0.27054,85.191,0.22599,-0.33099,0.91617,40.384,-0.17634,-0.93887,-0.29569,504.6
> view matrix models
> #7,0.9581,-0.19453,-0.21025,93.469,0.13432,-0.34319,0.92961,59.077,-0.25299,-0.9189,-0.30268,517.72
> view matrix models
> #7,0.95765,-0.21305,-0.19368,93.974,0.11202,-0.34399,0.93227,63.299,-0.26525,-0.91448,-0.30556,519.93
> hide #!3 models
> show #!3 models
> view matrix models
> #7,0.95696,-0.21706,-0.19263,94.734,0.10944,-0.34484,0.93226,64.012,-0.26878,-0.91322,-0.30625,520.54
> view matrix models
> #7,0.94815,-0.27392,-0.1612,101.89,0.14424,-0.081125,0.98621,-9.7554,-0.28322,-0.95833,-0.03741,476.68
> view matrix models
> #7,0.95414,-0.24037,-0.17843,97.229,0.16379,-0.079738,0.98327,-13.471,-0.25057,-0.9674,-0.036713,471.68
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.95414,-0.24037,-0.17843,96.447,0.16379,-0.079738,0.98327,-14.654,-0.25057,-0.9674,-0.036713,467.78
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99024,-0.071411,-0.11966,41.263,0.11264,-0.095331,0.98905,-2.0232,-0.082036,-0.99288,-0.086357,448.67
> view matrix models
> #7,0.99499,-0.013505,-0.099097,23.84,0.096797,-0.11921,0.98814,6.4479,-0.025158,-0.99278,-0.1173,443.37
> view matrix models
> #7,0.996,0.01454,-0.088107,15.449,0.089245,-0.12802,0.98775,9.9368,0.0030827,-0.99167,-0.1288,439.71
> view matrix models
> #7,0.99258,0.11362,-0.043338,-13.986,0.055935,-0.11014,0.99234,12.115,0.10798,-0.9874,-0.11568,414.38
> view matrix models
> #7,0.99638,0.054238,-0.065393,2.2931,0.06993,-0.086471,0.9938,3.9549,0.048247,-0.99478,-0.089951,422.89
> select subtract #7
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> fitmap #7 inMap #3
Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
steps = 140, shift = 3.54, angle = 8.85 degrees
Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99817702 -0.04588002 0.03921297 3.35030958
-0.04066443 -0.03114210 0.99868743 12.39857491
-0.04459863 -0.99846141 -0.03295101 431.82063884
Axis -0.99911720 0.04192858 0.00260921
Axis point 0.00000000 215.36415158 209.87663468
Rotation angle (degrees) 91.88869867
Shift along axis -1.70078525
> fitmap #7 inMap #3
Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
steps = 52, shift = 0.00236, angle = 0.00447 degrees
Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99817611 -0.04587745 0.03923922 3.34208981
-0.04068728 -0.03106753 0.99868882 12.38761501
-0.04459824 -0.99846385 -0.03287749 431.80589646
Axis -0.99911670 0.04194141 0.00259649
Axis point 0.00000000 215.36687767 209.87412872
Rotation angle (degrees) 91.88448023
Shift along axis -1.69840331
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> lighting soft
> lighting full
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> volume #7 level 0.22
> lighting simple
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!3 models
> close #144-146,148-154
> show #!162 models
> hide #!162 models
> close #162-165
> close #169-171
> show #!12 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> volume #13 level 0.04
> volume #13 level 0.02
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!14 models
> hide #!13 models
> volume #14 level 0.25
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!14 models
> hide #!11 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> show #2 models
> hide #2 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/I
Alignment identifier is 1/I
> select #1/I:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> color sel red
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #1
Nothing selected
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!19 models
> hide #!19 models
> close
> #19-21,76-84,91-97,136-140,142-143,155-156,158-159,161,166-168,172-173,175-176
> show #!178 models
> hide #!178 models
> show #!232 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> hide #!234 models
> show #!233 models
> hide #!233 models
> close #180-231
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> color #9 #d6d6d6ff models
> color #9 silver models
> color #9 darkgrey models
> color #9 #919191ff models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #2 models
> hide #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> show #!3 models
> select add #8
3 models selected
> select subtract #8
Nothing selected
> select add #8
3 models selected
> ui tool show "Color Actions"
> color sel light sea green
> select subtract #8
Nothing selected
> hide #!8 models
> show #!9 models
> select add #9
2 models selected
> color sel steel blue
> select subtract #9
Nothing selected
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #!3 models
> fitmap #13 inMap #3
Fit map cryosparc_P17_J1207_map_sharp.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 135754 points
correlation = 0.8195, correlation about mean = 0.6657, overlap = 1.259e+04
steps = 52, shift = 2.26, angle = 0.101 degrees
Position of cryosparc_P17_J1207_map_sharp.mrc z flip (#13) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99999956 -0.00066700 -0.00066264 0.29074301
0.00066701 0.99999978 0.00001245 -0.17783395
0.00066263 -0.00001289 0.99999978 -0.07194977
Axis -0.01347599 -0.70471591 0.70936161
Axis point 192.41646705 437.19131956 0.00000000
Rotation angle (degrees) 0.05387447
Shift along axis 0.07036596
> hide #!13 models
> show #!12 models
> fitmap #12 inMap #3
Fit map cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 178682 points
correlation = 0.9651, correlation about mean = 0.6584, overlap = 2.725e+05
steps = 56, shift = 2.37, angle = 0.0731 degrees
Position of cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip (#12)
relative to cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999939 0.00102607 0.00041428 -0.30090785
-0.00102640 0.99999915 0.00080313 0.12472239
-0.00041345 -0.00080355 0.99999959 0.19980920
Axis -0.58749376 0.30266385 -0.75049695
Axis point 102.26087289 256.35146195 0.00000000
Rotation angle (degrees) 0.07834647
Shift along axis 0.06457425
> hide #!12 models
> fitmap #14 inMap #3
Fit map cryosparc_P17_J1210_map_sharp.mrc z flip in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 113255 points
correlation = 0.9486, correlation about mean = 0.6387, overlap = 2.633e+04
steps = 52, shift = 2.43, angle = 0.0525 degrees
Position of cryosparc_P17_J1210_map_sharp.mrc z flip (#14) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
0.99999995 0.00019277 -0.00024648 0.02840578
-0.00019280 0.99999997 -0.00012225 0.02141418
0.00024646 0.00012230 0.99999996 -0.18912634
Axis 0.36395622 -0.73365042 -0.57384051
Axis point 527.18097402 0.00000000 -37.18039835
Rotation angle (degrees) 0.01924876
Shift along axis 0.10315629
> show #!14 models
> hide #!14 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!8 models
> hide #!11 models
> hide #2 models
> hide #!3 models
> show #!11 models
> show #!7 models
> combine #7
No structures specified
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
440,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
> volume #15 step 1
> volume #15 level 0.22
> select add #15
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,100.39,0,1,0,-46.513,0,0,1,45.903
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.80976,-0.45265,0.37335,153.4,0.3286,0.877,0.35057,-163.14,-0.48611,-0.1612,0.8589,208.93
> view matrix models
> #15,0.48179,-0.6745,0.5594,227.28,0.3403,0.73229,0.58987,-186.41,-0.80751,-0.093832,0.58234,319.83
> view matrix models
> #15,0.11088,-0.79909,0.5909,322.74,0.17639,0.60095,0.77958,-165.65,-0.97805,0.017785,0.20759,411.17
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.11088,-0.79909,0.5909,326.79,0.17639,0.60095,0.77958,-133.13,-0.97805,0.017785,0.20759,331.85
> view matrix models
> #15,0.11088,-0.79909,0.5909,305.76,0.17639,0.60095,0.77958,-140.24,-0.97805,0.017785,0.20759,332.58
> view matrix models
> #15,0.11088,-0.79909,0.5909,312.36,0.17639,0.60095,0.77958,-53.435,-0.97805,0.017785,0.20759,338.76
> view matrix models
> #15,0.11088,-0.79909,0.5909,308.51,0.17639,0.60095,0.77958,-56.402,-0.97805,0.017785,0.20759,338.76
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.024164,-0.79613,0.60464,332.95,0.20877,0.58746,0.78186,-60.832,-0.97767,0.14512,0.15201,324.44
> view matrix models
> #15,-0.11821,-0.78529,0.60774,349.54,0.18703,0.58347,0.7903,-57.299,-0.97522,0.20709,0.077898,326.9
> view matrix models
> #15,-0.105,-0.78677,0.60825,347,0.20205,0.58199,0.78769,-59.555,-0.97373,0.2056,0.097857,322.7
> view matrix models
> #15,-0.19293,-0.90299,-0.3839,597.45,0.097707,-0.40698,0.90819,138.04,-0.97633,0.13771,0.16675,322.58
> view matrix models
> #15,-0.14742,-0.90868,-0.3906,590.6,0.015659,-0.39701,0.91768,150.99,-0.98895,0.12916,0.072754,346.69
> view matrix models
> #15,-0.22245,-0.89505,-0.38653,602.49,0.048703,-0.40617,0.9125,147.11,-0.97373,0.18416,0.13394,319.48
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,572.78,0.083751,-0.20657,0.97484,86.116,-0.97098,0.20301,0.12644,316.65
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,576.09,0.083751,-0.20657,0.97484,-0.31383,-0.97098,0.20301,0.12644,309.91
> view matrix models
> #15,-0.22402,-0.95714,-0.18358,576.03,0.083751,-0.20657,0.97484,0.10503,-0.97098,0.20301,0.12644,306.13
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.2138,-0.95931,-0.18443,574.53,0.10809,-0.21087,0.97152,-3.3553,-0.97088,0.18777,0.14877,304.52
> view matrix models
> #15,-0.23097,-0.97294,-0.0055806,543.26,0.1557,-0.042623,0.98688,-50.688,-0.96042,0.22707,0.16133,291.71
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.23097,-0.97294,-0.0055806,539.65,0.1557,-0.042623,0.98688,-54.918,-0.96042,0.22707,0.16133,290.53
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.28101,-0.95968,0.0065516,544.75,0.21102,-0.055129,0.97593,-61.509,-0.93622,0.27563,0.21801,263.72
> hide #!15 models
> show #!15 models
> select subtract #15
Nothing selected
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!7 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> select add #15
2 models selected
> view matrix models
> #15,-0.25657,-0.95952,-0.11618,565.46,0.1776,-0.16496,0.97018,-31.028,-0.95007,0.22828,0.21274,277.33
> view matrix models
> #15,-0.2471,-0.95598,-0.15824,571.63,0.16674,-0.20281,0.96492,-19.967,-0.95454,0.21204,0.20951,282.24
> select subtract #15
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!11 models
> show #!177 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #243 models
> hide #243 models
> close #240-243
> show #!239 models
> hide #!239 models
> close #239
> close #237-238
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Tue Sep 3 13:30:10 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!3 models
> show #!3 models
> show #!232 models
> hide #!232 models
> show #!1 models
> hide #!177 models
> hide #!3 models
> hide #!15 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #20b2aa8f models
> set bgColor white
> color #8 #20b2aaa3 models
> color #8 #20b2aaab models
> color #8 #20b2aaae models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #20b2aa8a models
> show #!232 models
> hide #!8 models
> show #!8 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/L
Alignment identifier is 1/L
> select clear
> select #1/L:905-996
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> hide #!8 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> show #!1 models
> show #!8 models
> hide #!232 models
> lighting soft
> lighting full
> lighting simple
> hide #!1 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J535_003_volume_map_zflip.mrc
Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
588,588,588, pixel 0.95, shown at level 0.0831, step 4, values float32
> select add #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
> cofr sel
> select subtract #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> select add #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
> view sel
> select subtract #8
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> volume #16 step 1
> volume #16 level 0.2325
> select add #16
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 5 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.25096,-0.5068,-0.82472,635.54,0.24628,-0.85738,0.45193,125.51,-0.93614,-0.089699,0.33999,418.44,#16,0.38885,-0.060579,0.91931,48.211,-0.26865,0.94702,0.17604,66.153,-0.88126,-0.31542,0.35197,458.59
> view matrix models
> #1,-0.22215,-0.94943,-0.22187,455.62,0.42836,-0.29946,0.85254,-75.15,-0.87587,0.094354,0.47323,351.85,#16,-0.088966,0.51185,0.85446,2.4214,-0.38273,0.77443,-0.50376,264.06,-0.91957,-0.37184,0.127,524.01
> view matrix models
> #1,-0.38537,-0.9141,-0.12615,489.05,0.83574,-0.40371,0.37223,-86.716,-0.39118,0.038019,0.91953,35.134,#16,-0.26392,0.43198,0.8624,77.602,0.2312,0.89637,-0.37824,28.981,-0.93643,0.099556,-0.33645,444.31
> view matrix models
> #1,-0.1356,-0.57517,-0.80671,587.5,0.91613,-0.38283,0.11895,-42.958,-0.37725,-0.72292,0.57884,147.36,#16,0.44409,0.060297,0.89395,-3.9514,0.47456,0.83047,-0.29176,-31.753,-0.75999,0.5538,0.34018,134.84
> view matrix models
> #1,0.26845,-0.68107,-0.68124,397.8,0.89856,-0.077833,0.4319,-135.6,-0.34718,-0.72807,0.59108,132.33,#16,0.6063,0.40624,0.68364,-132.59,0.26507,0.70727,-0.65536,126.61,-0.74976,0.57856,0.32114,126.66
> view matrix models
> #1,0.38233,-0.62566,-0.67998,352.57,0.87609,0.011513,0.48201,-143.78,-0.29374,-0.78001,0.55254,124.4,#16,0.68689,0.42691,0.58816,-147.27,0.22309,0.64636,-0.72969,170.71,-0.69167,0.63243,0.34874,87.742
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.38233,-0.62566,-0.67998,380.63,0.87609,0.011513,0.48201,-254.96,-0.29374,-0.78001,0.55254,165.63,#16,0.68689,0.42691,0.58816,-119.21,0.22309,0.64636,-0.72969,59.535,-0.69167,0.63243,0.34874,128.97
> view matrix models
> #1,0.38233,-0.62566,-0.67998,289.1,0.87609,0.011513,0.48201,-274.53,-0.29374,-0.78001,0.55254,190.38,#16,0.68689,0.42691,0.58816,-210.74,0.22309,0.64636,-0.72969,39.961,-0.69167,0.63243,0.34874,153.72
> view matrix models
> #1,0.38233,-0.62566,-0.67998,298.14,0.87609,0.011513,0.48201,-272.93,-0.29374,-0.78001,0.55254,167.18,#16,0.68689,0.42691,0.58816,-201.7,0.22309,0.64636,-0.72969,41.57,-0.69167,0.63243,0.34874,130.51
> view matrix models
> #1,0.38233,-0.62566,-0.67998,282.73,0.87609,0.011513,0.48201,-276.94,-0.29374,-0.78001,0.55254,170.84,#16,0.68689,0.42691,0.58816,-217.11,0.22309,0.64636,-0.72969,37.554,-0.69167,0.63243,0.34874,134.18
> view matrix models
> #1,0.38233,-0.62566,-0.67998,281.94,0.87609,0.011513,0.48201,-275.2,-0.29374,-0.78001,0.55254,167.66,#16,0.68689,0.42691,0.58816,-217.9,0.22309,0.64636,-0.72969,39.291,-0.69167,0.63243,0.34874,130.99
> select subtract #16
625 atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
> ui tool show "Fit in Map"
> select add #1
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #1
Nothing selected
> fitmap #16 inMap #8
Fit map cryosparc_P17_J535_003_volume_map_zflip.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 276739 points
correlation = 0.9612, correlation about mean = 0.5525, overlap = 1.969e+04
steps = 164, shift = 2.78, angle = 15.9 degrees
Position of cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99998050 -0.00425494 -0.00457199 0.73851682
-0.00391421 -0.99738877 0.07211322 540.07003803
-0.00486689 -0.07209391 -0.99738598 573.94195717
Axis -0.99999512 0.00204496 0.00236281
Axis point 0.00000000 280.39509902 277.22388946
Rotation angle (degrees) 175.86516180
Shift along axis 1.72202130
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> fitmap #3 inMap #16
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J535_003_volume_map_zflip.mrc using 193604 points
correlation = 0.9176, correlation about mean = 0.2012, overlap = 2.042e+04
steps = 124, shift = 8.42, angle = 17.5 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) coordinates:
Matrix rotation and translation
0.58513310 0.56587388 -0.58086660 162.67581615
0.53803292 0.26503049 0.80017461 1.17881883
0.60674527 -0.78073400 -0.14938067 218.34134813
Axis -0.79945189 -0.60056511 -0.01407893
Axis point 0.00000000 55.92177713 150.33929755
Rotation angle (degrees) 98.60424165
Shift along axis -133.83346040
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #16
2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light sea green
> color sel cornflower blue
> color sel dark turquoise
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> color sel powder blue
> color sel light steel blue
> color sel pale turquoise
> color sel light blue
> color sel light sky blue
> select subtract #16
Nothing selected
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!3 models
> show #!8 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J655_005_volume_map_sharp.mrc
Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
588,588,588, pixel 0.95, shown at level 0.168, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
588,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
> volume #18 level 0.2742
> volume #18 step 1
> volume #18 level 0.4422
> volume #17 step 1
> volume #17 level 0.4266
> select add #17
2 models selected
> view matrix models #17,1,0,0,61.784,0,1,0,-62.478,0,0,1,-102.28
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.48945,0.25112,-0.83509,356.29,-0.79242,0.52783,-0.30572,377.6,0.36402,0.81137,0.45734,-292.7
> view matrix models
> #17,0.15791,0.038191,-0.98672,550.87,-0.45006,0.89221,-0.03749,107.36,0.87893,0.45,0.15807,-262.93
> view matrix models
> #17,-0.52223,0.57538,-0.62945,504.75,-0.48515,0.40657,0.77416,41.996,0.70136,0.70967,0.066821,-260.32
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,736.95,-0.72536,0.46156,0.5107,164.54,0.3622,0.88681,-0.28703,-119.76
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,769.33,-0.72536,0.46156,0.5107,134.03,0.3622,0.88681,-0.28703,-184.13
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,689.38,-0.72536,0.46156,0.5107,105.15,0.3622,0.88681,-0.28703,-37.942
> view matrix models
> #17,-0.58537,-0.023225,-0.81043,631.43,-0.72536,0.46156,0.5107,-28.227,0.3622,0.88681,-0.28703,-100.2
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.3388,-0.27569,-0.89956,653.75,-0.79784,0.59094,0.11938,58.328,0.49867,0.75815,-0.42016,-69.159
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.3388,-0.27569,-0.89956,660.19,-0.79784,0.59094,0.11938,89.728,0.49867,0.75815,-0.42016,-58.912
> fitmap #17 inMap #8
Fit map cryosparc_P17_J655_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 286513 points
correlation = 0.8688, correlation about mean = 0.2449, overlap = 8.66e+04
steps = 256, shift = 11.4, angle = 20.7 degrees
Position of cryosparc_P17_J655_005_volume_map_sharp.mrc (#17) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.95262622 -0.30211083 -0.03510445 642.60145687
0.17067519 -0.62654330 0.76046925 202.72382050
-0.25174046 0.71845148 0.64842440 -51.92560179
Axis -0.08053233 0.41521020 0.90615398
Axis point 303.70069952 160.23700769 0.00000000
Rotation angle (degrees) 164.87800612
Shift along axis -14.62978716
> select subtract #17
Nothing selected
> hide #!17 models
> show #!17 models
> show #!18 models
> select add #18
2 models selected
> view matrix models #18,1,0,0,64.318,0,1,0,-54.342,0,0,1,-66.309
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.21982,0.46975,-0.85499,506.62,-0.95518,0.074469,0.28649,397.56,0.19825,0.87965,0.43233,-216.22
> view matrix models
> #18,-0.94049,0.19544,-0.278,639.01,-0.33946,-0.50251,0.79514,246.97,0.015703,0.84219,0.53895,-181.2
> view matrix models
> #18,-0.54157,-0.62412,-0.56319,821.43,-0.82771,0.27878,0.487,253.66,-0.14694,0.7299,-0.66757,207.28
> view matrix models
> #18,-0.42526,-0.61847,-0.66079,811.74,-0.90422,0.2587,0.3398,319.03,-0.039206,0.742,-0.66925,173.54
> view matrix models
> #18,-0.94737,0.13657,-0.28954,659.99,-0.1521,0.60383,0.78247,-104.74,0.2817,0.78533,-0.55128,39.326
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,734.43,-0.3217,0.63403,0.70321,-43.906,0.13504,0.76582,-0.62871,106.65
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,676.58,-0.3217,0.63403,0.70321,-192.92,0.13504,0.76582,-0.62871,39.473
> view matrix models
> #18,-0.93716,-0.1073,-0.33199,622.9,-0.3217,0.63403,0.70321,-192.02,0.13504,0.76582,-0.62871,103.22
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.79577,-0.00053325,-0.6056,623.89,-0.55271,0.40935,0.72591,-70.483,0.24752,0.91238,-0.32605,-47.021
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.79577,-0.00053325,-0.6056,629.43,-0.55271,0.40935,0.72591,-66.36,0.24752,0.91238,-0.32605,-58.769
> fitmap #18 inMap #8
Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
correlation = 0.7365, correlation about mean = 0.04959, overlap = 5.271e+04
steps = 264, shift = 14.2, angle = 19.7 degrees
Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.98450205 -0.17536898 0.00119668 603.21178623
0.16771790 -0.93951186 0.29864389 420.47135877
-0.05124858 0.29421622 0.95436387 -43.01006329
Axis -0.01275615 0.15109534 0.98843689
Axis point 282.81965590 240.21101021 0.00000000
Rotation angle (degrees) 170.00569893
Shift along axis 13.32387113
> select subtract #18
Nothing selected
> hide #!18 models
> show #!18 models
> hide #!17 models
> select add #18
2 models selected
> view matrix models
> #18,-0.71292,0.17712,-0.6785,584.31,-0.44227,0.63729,0.63107,-109.78,0.54418,0.74999,-0.37601,-58.453
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.60845,0.16613,-0.77601,582.51,-0.56737,0.59263,0.57173,-46.453,0.55487,0.78815,-0.26633,-100.21
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,668.78,-0.55166,0.81473,0.17855,-9.9926,0.63987,0.55072,-0.53597,9.6575
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,676.27,-0.55166,0.81473,0.17855,-55.746,0.63987,0.55072,-0.53597,-8.0105
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,686.76,-0.55166,0.81473,0.17855,-55.075,0.63987,0.55072,-0.53597,-10.997
> view matrix models
> #18,-0.53501,-0.18143,-0.82514,683.39,-0.55166,0.81473,0.17855,-62.825,0.63987,0.55072,-0.53597,-15.419
> fitmap #18 inMap #8
Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
correlation = 0.8615, correlation about mean = 0.2577, overlap = 9.246e+04
steps = 124, shift = 4.79, angle = 8.22 degrees
Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.95287653 -0.30128223 -0.03543080 642.50639609
0.16990142 -0.62678199 0.76044582 202.97462428
-0.25131620 0.71859123 0.64843413 -52.01912235
Axis -0.08049372 0.41518546 0.90616874
Axis point 303.68746244 160.20985177 0.00000000
Rotation angle (degrees) 164.93072677
Shift along axis -14.58371648
> select subtract #18
Nothing selected
> hide #!18 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> volume #19 step 1
> volume #19 level 0.3083
> volume #19 level 0.349
> ui mousemode right "rotate selected models"
> select add #19
3 models selected
> view matrix models
> #19,-0.44408,0.45825,0.76993,46.649,-0.84084,-0.50996,-0.18146,698.91,0.30948,-0.72797,0.61178,228.1
> view matrix models
> #19,0.74377,0.47854,0.4667,-198.52,-0.1168,0.7805,-0.61415,275.9,-0.65815,0.40228,0.63641,182.36
> view matrix models
> #19,0.63923,-0.27239,0.71916,-40.675,0.75039,0.42547,-0.50585,98.912,-0.16819,0.86301,0.47637,-31.378
> view matrix models
> #19,0.48406,-0.45879,0.74511,45.429,0.87025,0.16344,-0.46471,124.56,0.091425,0.87338,0.47838,-107
> view matrix models
> #19,0.42748,-0.56077,0.70909,99.683,0.84962,-0.018802,-0.52707,198.53,0.30889,0.82776,0.4684,-152.09
> view matrix models
> #19,0.34186,-0.69155,0.63631,180.84,0.90812,0.068905,-0.41301,124.28,0.24177,0.71904,0.65156,-158.63
> view matrix models
> #19,0.71424,0.27698,0.64276,-188.14,0.046489,0.89756,-0.43844,146.08,-0.69835,0.34303,0.6282,212.11
> view matrix models
> #19,0.62219,0.51419,0.59033,-211.39,-0.24699,0.84448,-0.47524,253.15,-0.74288,0.14988,0.65243,269.79
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.62219,0.51419,0.59033,-152.75,-0.24699,0.84448,-0.47524,157.57,-0.74288,0.14988,0.65243,108.45
> view matrix models
> #19,0.62219,0.51419,0.59033,-232.8,-0.24699,0.84448,-0.47524,39.083,-0.74288,0.14988,0.65243,122.29
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.80455,0.20201,0.55847,-189.06,0.21173,0.78102,-0.58752,-37.641,-0.55486,0.59094,0.58559,-30.003
> view matrix models
> #19,0.66658,0.035494,0.74459,-161.06,0.34504,0.87073,-0.3504,-170.05,-0.66077,0.49048,0.56817,31.993
> view matrix models
> #19,0.69056,-0.011725,0.72318,-148.48,0.35206,0.87887,-0.32193,-182.74,-0.63181,0.47691,0.61104,14.806
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.69056,-0.011725,0.72318,-139.38,0.35206,0.87887,-0.32193,-182.11,-0.63181,0.47691,0.61104,39.587
> fitmap #19 inMap #8
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 437476 points
correlation = 0.926, correlation about mean = 0.3771, overlap = 9.23e+04
steps = 76, shift = 5.07, angle = 2.91 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99898029 -0.04235492 0.01563476 10.76195054
-0.02350758 -0.78361084 -0.62080710 683.98076137
0.03854581 0.61980652 -0.78380744 301.98502466
Axis 0.99971420 -0.01846223 0.01518761
Axis point 0.00000000 289.57241421 269.88486029
Rotation angle (degrees) 141.64850238
Shift along axis 2.71749516
> select subtract #19
Nothing selected
> hide #!8 models
> show #!17 models
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
588,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
> volume #20 step 1
> volume #20 level 0.1747
> volume #20 level 0.2443
> volume #21 step 1
> volume #21 level 0.2884
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #20
2 models selected
> select add #21
4 models selected
> view matrix models
> #20,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669,#21,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01,#21,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01
> view matrix models
> #20,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7,#21,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7
> view matrix models
> #20,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18,#21,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18
> view matrix models
> #20,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31,#21,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335,#21,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335
> view matrix models
> #20,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993,#21,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993
> hide #!19 models
> show #!8 models
> fitmap #20 inMap #8
Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 832636 points
correlation = 0.9229, correlation about mean = 0.5258, overlap = 1.189e+05
steps = 380, shift = 9.47, angle = 18.4 degrees
Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#20) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99901244 -0.04125012 0.01650989 10.10628769
-0.02203512 -0.78263856 -0.62208628 683.70365274
0.03858241 0.62110813 -0.78277461 301.46889960
Axis 0.99972305 -0.01774976 0.01545187
Axis point 0.00000000 289.37571004 269.89498614
Rotation angle (degrees) 141.55453890
Shift along axis 2.62616910
> hide #!21 models
> show #!21 models
> fitmap #21 inMap #8
Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 615528 points
correlation = 0.9307, correlation about mean = 0.4766, overlap = 1.046e+05
steps = 256, shift = 8.97, angle = 18.4 degrees
Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#21) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99901041 -0.04132365 0.01644837 10.15187435
-0.02212851 -0.78259628 -0.62213616 683.73846275
0.03858136 0.62115652 -0.78273626 301.42350706
Axis 0.99972248 -0.01779698 0.01543467
Axis point 0.00000000 289.39631274 269.89032870
Rotation angle (degrees) 141.55091738
Shift along axis 2.63294913
> select subtract #21
2 models selected
> select subtract #20
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!19 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> volume #19 level 0.3
> volume #20 level 0.3
> volume #21 level 0.3
> ui mousemode right zoom
> lighting soft
> hide #!20 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!19 models
> show #!19 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!21 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!21 models
> show #!177 models
> hide #!19 models
> show #!19 models
> fitmap #177 inMap #19
Fit molecule 6skl (#177) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
(#19) using 118220 atoms
average map value = 0.3221, steps = 64
shifted from previous position = 0.243
rotated from previous position = 0.297 degrees
atoms outside contour = 66812, contour level = 0.3
Position of 6skl (#177) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52950222 -0.10066174 -0.84231504 552.59666642
0.51811377 0.74784553 -0.41507252 112.80308239
0.67170345 -0.65619683 -0.34383163 339.58429947
Axis -0.14584759 -0.91577637 0.37427547
Axis point 163.10260363 0.00000000 350.04343026
Rotation angle (degrees) 124.24578811
Shift along axis -56.79921564
> hide #!19 models
> select add #177
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select subtract #177
Nothing selected
> color #19 #b2b2ff80 models
> color #19 #b2b2ffb4 models
> color #19 #b2b2ffbf models
> color #19 #b2b2ffd8 models
> color #19 #b2b2ffc6 models
> color #19 #b2b2ffc7 models
> set bgColor black
> set bgColor transparent
> hide #!177 models
> show #!177 models
> color #19 #b2b2ffff models
> color #19 #b2b2fffb models
> color #19 #b2b2ffff models
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!177 models
> show #!19 models
> show #!1 models
> hide #!1 models
> show #!177 models
> hide #!177 models
> show #!15 models
> hide #!15 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> ui tool show Matchmaker
> show #!1 models
> show #!177 models
> matchmaker #1/I to #177/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
score = 5322.6
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> select #1/8
6947 atoms, 7098 bonds, 7 pseudobonds, 859 residues, 3 models selected
> combine #1
> hide #!22 models
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> select #1/9
4594 atoms, 4699 bonds, 3 pseudobonds, 573 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!1 models
> set bgColor white
> set bgColor #ffffff00
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!177 models
> show #!177 models
> combine #177
[Repeated 2 time(s)]
> rename #23 6skl-Mcm2
> hide #!24 models
> hide #!25 models
> hide #!177 models
> hide #!23 models
> show #!23 models
> select #23/2
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> select ~sel & ##selected
107602 atoms, 108697 bonds, 122 pseudobonds, 6649 residues, 4 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> select add #23
10618 atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
> ui tool show "Color Actions"
> color sel hot pink
> show #!19 models
> color #19 #b2b2ffea models
> color #19 #b2b2ffde models
> color #19 #b2b2ffff models
> color #19 #b2b2ffdd models
> color #19 #b2b2ffd4 models
> hide #!19 models
> show #!19 models
> color #19 #b2b2ffff models
> select subtract #23
Nothing selected
> hide #!19 models
> show #!19 models
> color #19 #b2b2ff7f models
> color #19 #b2b2ffd4 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting full
> color #19 #b2b2ff82 models
> color #19 #b2b2ff90 models
> hide #!19 models
> show #!19 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!19 models
> combine #23
> ui tool show "Show Sequence Viewer"
> sequence chain #23/2
Alignment identifier is 23/2
> select clear
[Repeated 1 time(s)]
> select #23/2:173-442
4279 atoms, 4320 bonds, 270 residues, 1 model selected
> select #23/2:458-459
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #23/2:458-459
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #23/2:458
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #23/2:173-458
4533 atoms, 4577 bonds, 286 residues, 1 model selected
> select #23/2:466-467
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #23/2:173-467
4653 atoms, 4697 bonds, 295 residues, 1 model selected
> select #23/2:465-466
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #23/2:465-466
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #23/2:465
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #23/2:173-465
4631 atoms, 4675 bonds, 293 residues, 1 model selected
> select ~sel & ##selected
5987 atoms, 6033 bonds, 8 pseudobonds, 379 residues, 3 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> hide #!26 models
> rename #23 N-Mcm2_6skl
> show #!26 models
> hide #!23 models
> ui tool show "Show Sequence Viewer"
> sequence chain #26/2
Alignment identifier is 26/2
> select #26/2:466
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #26/2:466-868
5941 atoms, 5986 bonds, 1 pseudobond, 376 residues, 2 models selected
> select ~sel & ##selected
4677 atoms, 4722 bonds, 7 pseudobonds, 296 residues, 2 models selected
> delete atoms (#!26 & sel)
> delete bonds (#!26 & sel)
> rename #26 C-Mcm2_6skl
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!26 models
> show #!24 models
> lighting simple
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!26 models
> hide #!24 models
> show #!24 models
> select #25/3
9752 atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
> select add #25
118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
> select subtract #25
Nothing selected
> hide #!24 models
> show #!24 models
> select #24/3
9752 atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
> select ~sel & ##selected
108468 atoms, 109566 bonds, 123 pseudobonds, 6703 residues, 4 models selected
> delete atoms (#!24 & sel)
> delete bonds (#!24 & sel)
> rename #24 Mcm3_6skl
> combine #24
> ui tool show "Show Sequence Viewer"
> sequence chain #24/3
Alignment identifier is 24/3
> sequence chain #27/3
Alignment identifier is 27/3
> hide #!27 models
> select #24/3:332
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #24/3:18-332
4424 atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
> select ~sel & ##selected
5328 atoms, 5363 bonds, 6 pseudobonds, 336 residues, 3 models selected
> delete atoms (#!24 & sel)
> delete bonds (#!24 & sel)
> rename #24 N-Mcm3_6skl
> show #!27 models
> hide #!24 models
> select clear
> select #27/3:337-675
4320 atoms, 4351 bonds, 1 pseudobond, 275 residues, 2 models selected
> select clear
> select #27/3:337-740
5283 atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select ~sel & ##selected
4469 atoms, 4522 bonds, 5 pseudobonds, 284 residues, 3 models selected
> delete atoms (#!27 & sel)
> delete bonds (#!27 & sel)
> rename #27 C-Mcm3_6skl
> show #!24 models
> select add #27
5283 atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select add #24
9707 atoms, 9793 bonds, 3 pseudobonds, 616 residues, 4 models selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel cyan
[Repeated 1 time(s)]
> color sel turquoise
[Repeated 1 time(s)]
> color sel pale turquoise
[Repeated 4 time(s)]
> color sel turquoise
[Repeated 1 time(s)]
> select subtract #27
4424 atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
> select subtract #24
Nothing selected
> hide #!24 models
> hide #!27 models
> combine #177
[Repeated 1 time(s)]
> hide #!28 models
> hide #!29 models
> show #!25 models
> select #25/4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select #25/4
10883 atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
> select ~sel & ##selected
107337 atoms, 108453 bonds, 119 pseudobonds, 6641 residues, 4 models selected
> delete atoms (#!25 & sel)
> delete bonds (#!25 & sel)
> rename #25 Mcm4_6skl
> combine #25
> ui tool show "Show Sequence Viewer"
> sequence chain #25/4
Alignment identifier is 25/4
> sequence chain #30/4
Alignment identifier is 30/4
> hide #!30 models
> select #25/4:469
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/4:174-469
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> select ~sel & ##selected
6090 atoms, 6118 bonds, 11 pseudobonds, 384 residues, 3 models selected
> delete atoms (#!25 & sel)
> delete bonds (#!25 & sel)
> rename #25 N-Mcm4_6skl
> show #!30 models
> hide #!25 models
> select clear
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select #30/4:505-815
4436 atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
> select clear
> select #30/4:505-927
6089 atoms, 6118 bonds, 6 pseudobonds, 383 residues, 2 models selected
> select ~sel & ##selected
4794 atoms, 4834 bonds, 5 pseudobonds, 297 residues, 3 models selected
> delete atoms (#!30 & sel)
> delete bonds (#!30 & sel)
> rename #30 C-Mcm4_6skl
> show #!25 models
> select add #25
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> select add #30
10882 atoms, 10952 bonds, 6 pseudobonds, 679 residues, 3 models selected
> ui tool show "Color Actions"
> color sel forest green
> color sel sea green
> color sel turquoise
> color sel sea green
> color sel green
> color sel forest green
> color sel sea green
[Repeated 1 time(s)]
> select subtract #30
4793 atoms, 4834 bonds, 296 residues, 1 model selected
> hide #!30 models
> select subtract #25
Nothing selected
> hide #!25 models
> show #!28 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> select #28/5
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select ~sel & ##selected
108498 atoms, 109616 bonds, 119 pseudobonds, 6707 residues, 4 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> rename #28 Mcm5_6skl
> combine #28
> select add #28
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select add #31
19444 atoms, 19578 bonds, 22 pseudobonds, 1228 residues, 6 models selected
> ui tool show "Color Actions"
> color sel yellow
> select subtract #28
9722 atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
> select subtract #31
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #28/5
Alignment identifier is 28/5
> sequence chain #31/5
Alignment identifier is 31/5
> select #28/5:342
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #28/5:20-342
4172 atoms, 4202 bonds, 4 pseudobonds, 259 residues, 2 models selected
> select ~sel & ##selected
5550 atoms, 5587 bonds, 7 pseudobonds, 355 residues, 2 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> hide #!31 models
> rename #28 N-Mcm5_6skl
> show #!25 models
> show #!30 models
> hide #!30 models
> hide #!25 models
> show #!31 models
> hide #!31 models
> hide #!28 models
> show #!31 models
> select #31/5:343
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #31/5:343-694
5504 atoms, 5540 bonds, 352 residues, 1 model selected
> select ~sel & ##selected
4218 atoms, 4249 bonds, 11 pseudobonds, 262 residues, 3 models selected
> delete atoms (#!31 & sel)
> delete bonds (#!31 & sel)
> rename #31 C-Mcm5_6skl
> show #!28 models
> hide #!28 models
> hide #!31 models
> combine #177
> hide #!32 models
> show #!29 models
> select #29/6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select #29/6
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select ~sel & ##selected
108175 atoms, 109279 bonds, 121 pseudobonds, 6683 residues, 4 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> rename #29 Mcm6_6skl
> combine #29
> select add #29
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select add #33
20090 atoms, 20252 bonds, 18 pseudobonds, 1276 residues, 6 models selected
> ui tool show "Color Actions"
> color sel orange
> color sel dark orange
> color sel orange
> color sel dark orange
[Repeated 1 time(s)]
> color sel goldenrod
> color sel dark orange
> color sel sandy brown
> color sel dark orange
[Repeated 1 time(s)]
> select subtract #29
10045 atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
> select subtract #33
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #29/6
Alignment identifier is 29/6
> sequence chain #33/6
Alignment identifier is 33/6
> select #29/6:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #29/6:459-463
72 atoms, 71 bonds, 5 residues, 1 model selected
> select
> #29/6:98-102,105-122,134-147,155-161,164-193,277-284,384-386,407-411,500-521,524-533,540-553,580-592,604-609,626-631,640-650,652-658,694-699,702-707,720-735,747-759,766-784,796-814,820-836
4489 atoms, 4500 bonds, 275 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #29/6:91-463
4862 atoms, 4908 bonds, 2 pseudobonds, 305 residues, 2 models selected
> select ~sel & ##selected
5183 atoms, 5218 bonds, 7 pseudobonds, 333 residues, 3 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> rename #29 N-Mcm6_6skl
> hide #!29 models
> show #!29 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!28 models
> show #!31 models
> hide #!31 models
> hide #!29 models
> hide #!28 models
> show #!28 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #!28 models
> show #!31 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #!31 models
> show #!29 models
> show #!33 models
> show #!28 models
> hide #!28 models
> hide #!33 models
> show #!33 models
> hide #!29 models
> select clear
[Repeated 2 time(s)]
> select #33/6:497-838
5182 atoms, 5218 bonds, 2 pseudobonds, 332 residues, 2 models selected
> select ~sel & ##selected
4863 atoms, 4908 bonds, 7 pseudobonds, 306 residues, 3 models selected
> delete atoms (#!33 & sel)
> delete bonds (#!33 & sel)
> rename #33 C-Mcm6_6skl
> show #!29 models
> hide #!29 models
> hide #!33 models
> show #!32 models
> select #32/7
9981 atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
> select ~sel & ##selected
108239 atoms, 109350 bonds, 119 pseudobonds, 6685 residues, 4 models selected
> delete atoms (#!32 & sel)
> delete bonds (#!32 & sel)
> select add #32
9981 atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
> rename #32 Mcm7_6skl
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> select subtract #32
Nothing selected
> combine #32
> ui tool show "Show Sequence Viewer"
> sequence chain #32/7
Alignment identifier is 32/7
> sequence chain #34/7
Alignment identifier is 34/7
> ui tool show "Show Sequence Viewer"
> sequence chain #32/7
Destroying pre-existing alignment with identifier 32/7
Alignment identifier is 32/7
> sequence chain #34/7
Destroying pre-existing alignment with identifier 34/7
Alignment identifier is 34/7
> select #32/7:385
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #32/7:4-385
4942 atoms, 4986 bonds, 3 pseudobonds, 317 residues, 2 models selected
> select ~sel & ##selected
5039 atoms, 5069 bonds, 8 pseudobonds, 319 residues, 3 models selected
> delete atoms (#!32 & sel)
> delete bonds (#!32 & sel)
> rename #32 N-Mcm7_6skl
> select clear
> select #34/7:396-729
5038 atoms, 5069 bonds, 3 pseudobonds, 318 residues, 2 models selected
> select ~sel & ##selected
4943 atoms, 4986 bonds, 8 pseudobonds, 318 residues, 3 models selected
> delete atoms (#!34 & sel)
> delete bonds (#!34 & sel)
> rename #34 C-Mcm7_6skl
> hide #!34 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!34 models
> hide #!34 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> combine #177
[Repeated 3 time(s)]
> hide #!36 models
> hide #!37 models
> hide #!38 models
> hide #!35 models
> show #!23 models
> show #!24 models
> show #!25 models
> show #!26 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> show #!32 models
> show #!33 models
> show #!34 models
> hide #!34 models
> hide #!33 models
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!35 models
> select #35/E
9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
> select ~sel & ##selected
109091 atoms, 110192 bonds, 126 pseudobonds, 6757 residues, 4 models selected
> delete atoms (#!35 & sel)
> delete bonds (#!35 & sel)
> rename #35 Cdc45_6skl
> select add #35
9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light cyan
[Repeated 1 time(s)]
> color sel powder blue
> color sel light blue
[Repeated 1 time(s)]
> color sel light cyan
> select subtract #35
Nothing selected
> lighting soft
[Repeated 1 time(s)]
> lighting full
> hide #!35 models
> show #!36 models
> lighting simple
> select #36/A,B,C,D
13385 atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
> select ~sel & ##selected
104835 atoms, 105897 bonds, 124 pseudobonds, 6511 residues, 4 models selected
> delete atoms (#!36 & sel)
> delete bonds (#!36 & sel)
> select add #36
13385 atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
> rename #36 GINS_6skl
> ui tool show "Color Actions"
> color sel silver
> color sel gray
> select clear
> hide #!36 models
> show #!37 models
> select #37/F,G,H
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> select ~sel & ##selected
97999 atoms, 98929 bonds, 124 pseudobonds, 6050 residues, 4 models selected
> delete atoms (#!37 & sel)
> delete bonds (#!37 & sel)
> select add #37
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> ui tool show "Color Actions"
> color sel slate blue
> color sel medium slate blue
[Repeated 3 time(s)]
> color sel royal blue
> color sel dodger blue
> color sel royal blue
[Repeated 1 time(s)]
> color sel dodger blue
> color sel royal blue
> select subtract #37
Nothing selected
> show #!32 models
> hide #!32 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> rename #37 Ctf4_6skl
> combine #177
> hide #!39 models
> show #!38 models
> select #38/X
10990 atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
> select ~sel & ##selected
107230 atoms, 108313 bonds, 123 pseudobonds, 6656 residues, 4 models selected
> delete atoms (#!38 & sel)
> delete bonds (#!38 & sel)
> rename #38 Tof1_6skl
> select add #38
10990 atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
> ui tool show "Color Actions"
> color sel slate blue
> color sel medium slate blue
> color sel royal blue
> color sel medium slate blue
[Repeated 7 time(s)]
> color sel dark slate blue
> color sel medium slate blue
> select subtract #38
Nothing selected
> hide #!38 models
> show #!38 models
> show #!39 models
> hide #!38 models
> select #39/Y
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> select ~sel & ##selected
116604 atoms, 117773 bonds, 130 pseudobonds, 7227 residues, 4 models selected
> delete atoms (#!39 & sel)
> delete bonds (#!39 & sel)
> rename #39 Csm3_6skl
> select add #39
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> hide #!39 models
> select subtract #39
Nothing selected
> show #!39 models
> show #!38 models
> show #!37 models
> show #!36 models
> show #!35 models
> show #!34 models
> show #!33 models
> show #!32 models
> show #!31 models
> show #!30 models
> show #!29 models
> show #!28 models
> show #!27 models
> show #!26 models
> show #!25 models
> show #!24 models
> show #!23 models
> select add #39
1616 atoms, 1632 bonds, 94 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel blue violet
> color sel deep pink
> color sel magenta
> color sel dark magenta
> color sel purple
[Repeated 1 time(s)]
> color sel dark magenta
> color sel purple
[Repeated 1 time(s)]
> color sel medium purple
> color sel purple
[Repeated 1 time(s)]
> select subtract #39
Nothing selected
> combine #177
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!34 models
> hide #!33 models
> hide #!40 models
> show #!35 models
> hide #!35 models
> hide #!34 models
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!40 models
> select #40/I,J
1878 atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
> select ~sel & ##selected
116342 atoms, 117390 bonds, 80 pseudobonds, 7262 residues, 3 models selected
> delete atoms (#!40 & sel)
> delete bonds (#!40 & sel)
> rename #40 DNA_6skl
> select #40/I
1192 atoms, 1279 bonds, 37 residues, 1 model selected
> color sel black
> select #40/J
686 atoms, 736 bonds, 22 residues, 1 model selected
> color sel dim gray
> select clear
> hide #!40 models
> show #!19 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!19 models
> show #!24 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> show #!23 models
> show #!19 models
> fitmap #23 inMap #19
Fit molecule N-Mcm2_6skl (#23) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
average map value = 0.4542, steps = 52
shifted from previous position = 1.09
rotated from previous position = 3.28 degrees
atoms outside contour = 1773, contour level = 0.3
Position of N-Mcm2_6skl (#23) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.48619287 -0.07981194 -0.87019915 544.75612919
0.53368692 0.76140981 -0.36801274 98.39251819
0.69194998 -0.64333907 -0.32759742 329.31388927
Axis -0.16188679 -0.91851479 0.36072599
Axis point 157.28465121 0.00000000 346.27079505
Rotation angle (degrees) 121.74840423
Shift along axis -59.77172713
> fitmap #23 inMap #19
Fit molecule N-Mcm2_6skl (#23) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
average map value = 0.4542, steps = 36
shifted from previous position = 0.0153
rotated from previous position = 0.0153 degrees
atoms outside contour = 1772, contour level = 0.3
Position of N-Mcm2_6skl (#23) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.48612668 -0.08005636 -0.87021368 544.79200838
0.53355946 0.76145094 -0.36811244 98.44034714
0.69209476 -0.64326002 -0.32744679 329.22783276
Axis -0.16176651 -0.91852227 0.36076090
Axis point 157.31175798 0.00000000 346.27934228
Rotation angle (degrees) 121.73971426
Shift along axis -59.77622153
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> fitmap #24 inMap #19
Fit molecule N-Mcm3_6skl (#24) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4424 atoms
average map value = 0.4899, steps = 72
shifted from previous position = 1.7
rotated from previous position = 1.03 degrees
atoms outside contour = 1496, contour level = 0.3
Position of N-Mcm3_6skl (#24) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51684057 -0.09904554 -0.85033277 552.53192555
0.53049272 0.74253315 -0.40892786 109.84096466
0.67190275 -0.66244585 -0.33122832 337.40029650
Axis -0.15211044 -0.91333918 0.37772207
Axis point 161.67410853 0.00000000 351.20284420
Rotation angle (degrees) 123.55710836
Shift along axis -56.92439016
> hide #!24 models
> show #!25 models
> fitmap #25 inMap #19
Fit molecule N-Mcm4_6skl (#25) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4793 atoms
average map value = 0.4529, steps = 52
shifted from previous position = 2.33
rotated from previous position = 1.94 degrees
atoms outside contour = 1614, contour level = 0.3
Position of N-Mcm4_6skl (#25) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51485483 -0.08657680 -0.85289447 549.29032703
0.51292450 0.76605243 -0.38739145 104.77742894
0.68690099 -0.63692082 -0.34999843 331.94917409
Axis -0.14931878 -0.92141613 0.35874256
Axis point 162.77097442 0.00000000 344.51466083
Rotation angle (degrees) 123.32588851
Shift along axis -59.47868024
> hide #!25 models
> show #!28 models
> fitmap #28 inMap #19
Fit molecule N-Mcm5_6skl (#28) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4172 atoms
average map value = 0.5001, steps = 48
shifted from previous position = 0.477
rotated from previous position = 0.518 degrees
atoms outside contour = 1491, contour level = 0.3
Position of N-Mcm5_6skl (#28) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52208241 -0.10009271 -0.84700143 552.10007852
0.52281543 0.74707399 -0.41054169 110.98680483
0.67386497 -0.65716201 -0.33770418 337.87117097
Axis -0.14839770 -0.91514390 0.37481963
Axis point 162.27606171 0.00000000 350.25308806
Rotation angle (degrees) 123.80418376
Shift along axis -56.85853328
> hide #!28 models
> show #!29 models
> fitmap #29 inMap #19
Fit molecule N-Mcm6_6skl (#29) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4862 atoms
average map value = 0.4386, steps = 64
shifted from previous position = 1.82
rotated from previous position = 1.81 degrees
atoms outside contour = 1794, contour level = 0.3
Position of N-Mcm6_6skl (#29) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50972104 -0.08434926 -0.85619488 547.63107126
0.52443527 0.75845239 -0.38693363 104.75971281
0.68202061 -0.64624700 -0.34236341 333.92722557
Axis -0.15485966 -0.91860876 0.36356077
Axis point 160.21705818 0.00000000 346.31455571
Rotation angle (degrees) 123.14885220
Shift along axis -59.63631555
> hide #!29 models
> show #!32 models
> fitmap #32 inMap #19
Fit molecule N-Mcm7_6skl (#32) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4942 atoms
average map value = 0.4432, steps = 72
shifted from previous position = 2.55
rotated from previous position = 2 degrees
atoms outside contour = 1716, contour level = 0.3
Position of N-Mcm7_6skl (#32) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50209844 -0.09646270 -0.85941382 551.56164113
0.52217420 0.75834411 -0.39019012 105.12547600
0.68937019 -0.64467757 -0.33039306 330.21496061
Axis -0.15084576 -0.91803150 0.36669294
Axis point 162.01873803 0.00000000 348.31963616
Rotation angle (degrees) 122.48465413
Shift along axis -58.62173799
> hide #!32 models
> show #!26 models
> hide #!26 models
> show #!27 models
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 68
shifted from previous position = 2.23
rotated from previous position = 2.57 degrees
atoms outside contour = 3746, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49125191 -0.10951013 -0.86410596 552.71575277
0.52980778 0.74986873 -0.39623302 105.24621685
0.69135757 -0.65246028 -0.31035512 328.13372850
Axis -0.15062172 -0.91437023 0.37581934
Axis point 161.23471230 0.00000000 351.59387631
Rotation angle (degrees) 121.72677225
Shift along axis -56.16600219
> hide #!27 models
> show #!26 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> fitmap #26 inMap #19
Fit molecule C-Mcm2_6skl (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
average map value = 0.2499, steps = 120
shifted from previous position = 7.11
rotated from previous position = 16.9 degrees
atoms outside contour = 4089, contour level = 0.3
Position of C-Mcm2_6skl (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.72499338 -0.17926092 -0.66501889 564.61757623
0.30570305 0.78146839 -0.54392354 172.58562424
0.61719547 -0.59763926 -0.51175880 374.68531048
Axis -0.03915385 -0.93461689 0.35349433
Axis point 195.27960459 0.00000000 339.48855257
Rotation angle (degrees) 136.68906839
Shift along axis -50.95925582
> hide #!26 models
> show #!27 models
> hide #!27 models
> show #!30 models
> hide #!30 models
> show #!31 models
> fitmap #31 inMap #19
Fit molecule C-Mcm5_6skl (#31) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5504 atoms
average map value = 0.2192, steps = 72
shifted from previous position = 1.38
rotated from previous position = 0.644 degrees
atoms outside contour = 4241, contour level = 0.3
Position of C-Mcm5_6skl (#31) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.52798995 -0.11167009 -0.84187672 553.62723896
0.51297984 0.74809912 -0.42095058 113.66344352
0.67681482 -0.65412346 -0.33770431 336.54923223
Axis -0.14058346 -0.91564213 0.37661090
Axis point 164.28052383 0.00000000 350.23415639
Rotation angle (degrees) 123.97268209
Shift along axis -55.15775830
> hide #!31 models
> show #!32 models
> hide #!32 models
> show #!33 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> fitmap #33 inMap #19
Fit molecule C-Mcm6_6skl (#33) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5182 atoms
average map value = 0.2506, steps = 100
shifted from previous position = 2.49
rotated from previous position = 3.08 degrees
atoms outside contour = 3615, contour level = 0.3
Position of C-Mcm6_6skl (#33) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.56822296 -0.11833571 -0.81432140 555.66185955
0.48213507 0.75407081 -0.44600784 124.85237619
0.66683465 -0.64604479 -0.37142655 342.86696321
Axis -0.12419139 -0.91956426 0.37279763
Axis point 169.39701035 0.00000000 347.59627562
Rotation angle (degrees) 126.35519939
Shift along axis -55.99821082
> hide #!33 models
> show #!34 models
> fitmap #34 inMap #19
Fit molecule C-Mcm7_6skl (#34) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
average map value = 0.2488, steps = 84
shifted from previous position = 3.58
rotated from previous position = 6.44 degrees
atoms outside contour = 3687, contour level = 0.3
Position of C-Mcm7_6skl (#34) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.60810284 -0.04397762 -0.79263921 541.80870758
0.49024443 0.76452307 -0.41852703 112.51289532
0.62439678 -0.64309443 -0.44334887 361.42999934
Axis -0.14668479 -0.92559125 0.34894756
Axis point 166.00281620 0.00000000 336.12434083
Rotation angle (degrees) 130.05063287
Shift along axis -57.49592849
> hide #!34 models
> show #!26 models
> fitmap #26 inMap #19
Fit molecule C-Mcm2_6skl (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
average map value = 0.2499, steps = 40
shifted from previous position = 0.00827
rotated from previous position = 0.0158 degrees
atoms outside contour = 4089, contour level = 0.3
Position of C-Mcm2_6skl (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.72508101 -0.17912737 -0.66495934 564.59530186
0.30560205 0.78160601 -0.54378253 172.54320727
0.61714254 -0.59749932 -0.51198599 374.71726789
Axis -0.03915999 -0.93466297 0.35337179
Axis point 195.28291115 0.00000000 339.45035239
Rotation angle (degrees) 136.69646920
Shift along axis -50.96478166
> hide #!26 models
> show #!27 models
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 48
shifted from previous position = 0.00561
rotated from previous position = 0.0144 degrees
atoms outside contour = 3745, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49119447 -0.10962931 -0.86412349 552.72708725
0.52963562 0.75000136 -0.39621215 105.24134461
0.69153026 -0.65228780 -0.31033293 328.08057761
Axis -0.15052098 -0.91441153 0.37575921
Axis point 161.25504150 0.00000000 351.58454506
Rotation angle (degrees) 121.71962364
Shift along axis -56.15162171
> fitmap #27 inMap #19
Fit molecule C-Mcm3_6skl (#27) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
average map value = 0.2453, steps = 44
shifted from previous position = 0.00644
rotated from previous position = 0.00323 degrees
atoms outside contour = 3747, contour level = 0.3
Position of C-Mcm3_6skl (#27) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.49121423 -0.10960226 -0.86411569 552.72290598
0.52966978 0.74997300 -0.39622018 105.24674287
0.69149006 -0.65232495 -0.31034441 328.08956470
Axis -0.15054136 -0.91440312 0.37577152
Axis point 161.25087455 0.00000000 351.58379235
Rotation angle (degrees) 121.72163061
Shift along axis -56.15889268
> hide #!27 models
> show #!33 models
> hide #!33 models
> show #!34 models
> fitmap #34 inMap #19
Fit molecule C-Mcm7_6skl (#34) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
average map value = 0.2488, steps = 40
shifted from previous position = 0.021
rotated from previous position = 0.0237 degrees
atoms outside contour = 3683, contour level = 0.3
Position of C-Mcm7_6skl (#34) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.60807905 -0.04366734 -0.79267461 541.74998075
0.49057375 0.76436052 -0.41843804 112.46427092
0.62416126 -0.64330876 -0.44336957 361.50164606
Axis -0.14689577 -0.92554158 0.34899056
Axis point 165.95199356 0.00000000 336.12532515
Rotation angle (degrees) 130.05660056
Shift along axis -57.51048000
> hide #!34 models
> show #!35 models
> fitmap #35 inMap #19
Fit molecule Cdc45_6skl (#35) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 9129 atoms
average map value = 0.4936, steps = 32
shifted from previous position = 0.989
rotated from previous position = 0.293 degrees
atoms outside contour = 3011, contour level = 0.3
Position of Cdc45_6skl (#35) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53238330 -0.10222439 -0.84030840 552.34452064
0.51398389 0.74970935 -0.41684104 113.43549525
0.67259838 -0.65382418 -0.34659105 340.11300103
Axis -0.14356656 -0.91653277 0.37330461
Axis point 163.36596759 0.00000000 349.77928908
Rotation angle (degrees) 124.37677529
Shift along axis -56.29979678
> hide #!35 models
> show #!36 models
> fitmap #36 inMap #19
Fit molecule GINS_6skl (#36) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 13385 atoms
average map value = 0.5009, steps = 64
shifted from previous position = 1.25
rotated from previous position = 0.693 degrees
atoms outside contour = 4520, contour level = 0.3
Position of GINS_6skl (#36) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53440728 -0.10575367 -0.83858514 554.21323619
0.51997798 0.74104668 -0.42482082 114.22988038
0.66635709 -0.66307314 -0.34103116 341.67599231
Axis -0.14464380 -0.91365555 0.37988381
Axis point 163.82286606 0.00000000 351.69409164
Rotation angle (degrees) 124.55491640
Shift along axis -54.73309110
> hide #!36 models
> show #!37 models
> fitmap #37 inMap #19
Fit molecule Ctf4_6skl (#37) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 20221 atoms
average map value = 0.3967, steps = 68
shifted from previous position = 1.75
rotated from previous position = 0.685 degrees
atoms outside contour = 7725, contour level = 0.3
Position of Ctf4_6skl (#37) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.53679956 -0.10566869 -0.83706653 554.09013415
0.51701361 0.74282869 -0.42532631 116.11912844
0.66674070 -0.66108976 -0.34411796 343.05037030
Axis -0.14335492 -0.91438332 0.37861921
Axis point 163.58631600 0.00000000 352.06583111
Rotation angle (degrees) 124.68361653
Shift along axis -55.72348034
> hide #!37 models
> show #!38 models
> fitmap #38 inMap #19
Fit molecule Tof1_6skl (#38) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 10990 atoms
average map value = 0.3486, steps = 52
shifted from previous position = 2.71
rotated from previous position = 2.1 degrees
atoms outside contour = 4840, contour level = 0.3
Position of Tof1_6skl (#38) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.50884095 -0.07790103 -0.85732860 546.87430545
0.52700003 0.75928729 -0.38177714 104.30156172
0.68069954 -0.64607604 -0.34530262 334.50800166
Axis -0.15791244 -0.91893600 0.36141430
Axis point 159.52485154 0.00000000 345.83620169
Rotation angle (degrees) 123.19075103
Shift along axis -61.30873983
> hide #!38 models
> show #!39 models
> fitmap #39 inMap #19
Fit molecule Csm3_6skl (#39) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 1616 atoms
average map value = 0.3779, steps = 60
shifted from previous position = 2.5
rotated from previous position = 1.9 degrees
atoms outside contour = 645, contour level = 0.3
Position of Csm3_6skl (#39) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.51530602 -0.07349129 -0.85384937 547.02376900
0.53880358 0.74699785 -0.38946748 106.53379719
0.66644611 -0.66075203 -0.34533512 340.04339220
Axis -0.16330007 -0.91514372 0.36857164
Axis point 158.27460801 0.00000000 348.00938205
Rotation angle (degrees) 123.83627701
Shift along axis -61.49240111
> hide #!39 models
> show #!40 models
> fitmap #40 inMap #19
Fit molecule DNA_6skl (#40) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
(#19) using 1878 atoms
average map value = 0.3403, steps = 80
shifted from previous position = 1.35
rotated from previous position = 3.78 degrees
atoms outside contour = 831, contour level = 0.3
Position of DNA_6skl (#40) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
Matrix rotation and translation
-0.47993510 -0.10126507 -0.87144001 550.20291579
0.51412450 0.77241029 -0.37290528 101.33591686
0.71087151 -0.62699899 -0.31864396 321.37532285
Axis -0.14801492 -0.92172967 0.35847734
Axis point 161.49135847 0.00000000 346.98780116
Rotation angle (degrees) 120.86949809
Shift along axis -59.63678931
> hide #!40 models
> show #!40 models
> hide #!40 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> combine #23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40
Remapping chain ID '2' in C-Mcm2_6skl #26 to '5'
Remapping chain ID '3' in C-Mcm3_6skl #27 to '6'
Remapping chain ID '5' in N-Mcm5_6skl #28 to '7'
Remapping chain ID '6' in N-Mcm6_6skl #29 to '8'
Remapping chain ID '4' in C-Mcm4_6skl #30 to '9'
Remapping chain ID '5' in C-Mcm5_6skl #31 to '0'
Remapping chain ID '7' in N-Mcm7_6skl #32 to 'AA'
Remapping chain ID '6' in C-Mcm6_6skl #33 to 'AB'
Remapping chain ID '7' in C-Mcm7_6skl #34 to 'AC'
> hide #!19 models
> select add #41
118080 atoms, 119265 bonds, 97 pseudobonds, 7310 residues, 3 models selected
> cartoon style (#!41 & sel) xsection oval modeHelix default
> cartoon style (#!41 & sel) xsection rectangle modeHelix default
> cartoon style (#!41 & sel & coil) xsection oval
> cartoon style (#!41 & sel) xsection barbell modeHelix default
> cartoon style (#!41 & sel) xsection oval modeHelix default
> cartoon hide (#!41 & sel)
> show (#!41 & sel) target ab
> ui tool show "Color Zone"
> select subtract #41
Nothing selected
> hide #!41 models
> show #!19 models
> color #19 #b2b2ffff models
> volume copy #19
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!42 models
> show #!42 models
> show #!41 models
> hide #!41 models
> ui tool show "Hide Dust"
> surface dust #42 size 5.7
> surface dust #42 size 5.67
> surface dust #42 size 6.93
> surface dust #42 size 7.1
> surface dust #42 size 5.86
> surface dust #42 size 5.91
> surface dust #42 size 6.71
> show #!41 models
> color zone #42 near #41 distance 5.7
> hide #!41 models
> lighting soft
> lighting simple
> graphics silhouettes true
> color zone #42 near #41 distance 5.8
> color zone #42 near #41 distance 5.9
> show #!41 models
> color zone #42 near #41 distance 5.9
> color zone #42 near #41 distance 6.2
> color zone #42 near #41 distance 7.58
> color zone #42 near #41 distance 6.79
> color zone #42 near #41 distance 10.77
> color zone #42 near #41 distance 11.05
> color zone #42 near #41 distance 8.88
> color zone #42 near #41 distance 10.95
> color zone #42 near #41 distance 9.58
> hide #!42 models
> show #!42 models
> color zone #42 near #41 distance 9.68
> color zone #42 near #41 distance 9.6
> color zone #42 near #41 distance 9
> color zone #42 near #41 distance 9.9
> color zone #42 near #41 distance 9.99
> color zone #42 near #41 distance 10.42
> color zone #42 near #41 distance 11.42
> hide #!42 models
> show #!42 models
> lighting soft
> hide #!41 models
> hide #!42 models
> show #!42 models
> lighting simple
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
[Repeated 1 time(s)]
\u2014\u2014\u2014 End of log from Wed Sep 4 05:32:36 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> lighting full
> lighting soft
> lighting simple
> show #2 models
> hide #2 models
> show #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!22 models
> hide #!22 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!3 models
> show #!3 models
> combine #1
> hide #!1 models
> show #!22 models
> hide #!22 models
> rename #22 8xgc_with_polE
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> select #43/L,M,P,Q,N,R,O,S
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> hide (#!43 & sel) target a
> cartoon hide (#!43 & sel)
> hide #2 models
> show #2 models
> hide #2 models
> cartoon (#!43 & sel)
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> hide #!43 models
> show #!43 models
> select #43/2,I
12246 atoms, 12460 bonds, 7 pseudobonds, 1525 residues, 3 models selected
> select ~sel & ##selected
49582 atoms, 50669 bonds, 146 pseudobonds, 6085 residues, 4 models selected
> select #43/2,I,X,Y
14083 atoms, 14513 bonds, 93 pseudobonds, 1615 residues, 4 models selected
> select ~sel & ##selected
47745 atoms, 48616 bonds, 60 pseudobonds, 5995 residues, 3 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> hide #!43 models
> show #!43 models
> rename #43 Tof1_Mcm2_DNA_8xgc
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> hide #!43 models
> show #!43 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> ui tool show "Fit in Map"
> hide #!3 models
> show #!3 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> fitmap #3 inMap #8
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 193604 points
correlation = 0.9192, correlation about mean = 0.0445, overlap = 1.418e+04
steps = 72, shift = 2.72, angle = 2.42 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
to cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.59052855 0.53373057 -0.60531621 170.37442141
-0.50876033 -0.33602858 -0.79262080 554.64399601
-0.62644949 0.77602608 0.07310647 351.56427577
Axis 0.83279921 0.01121972 -0.55346146
Axis point 0.00000000 138.28597245 467.32476580
Rotation angle (degrees) 109.64532984
Shift along axis -46.46664408
> hide #!8 models
> show #!232 models
> hide #!232 models
> show #!234 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> hide #!234 models
> show #!234 models
> hide #!3 models
> show #!3 models
> fitmap #234 inMap #3
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) using 6114 atoms
average map value = 0.2545, steps = 96
shifted from previous position = 4.78
rotated from previous position = 8.84 degrees
atoms outside contour = 2956, contour level = 0.25
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
Matrix rotation and translation
-0.05320350 -0.99827136 0.02497348 191.32301696
-0.66299192 0.05401395 0.74667544 251.48569117
-0.74673362 0.02316853 -0.66471958 182.33677195
Axis -0.65199157 0.69542739 0.30213861
Axis point 246.33178982 0.00000000 -20.06616176
Rotation angle (degrees) 146.30004573
Shift along axis 105.24002362
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> hide #!234 models
> show #!177 models
> hide #!177 models
> show #!232 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #43/x
1041 atoms, 1159 bonds, 51 residues, 1 model selected
> color sel black
> select #43/y
796 atoms, 894 bonds, 39 residues, 1 model selected
> color sel gray
> select clear
> select #232/J
3004 atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
> color (#!232 & sel) black
> select #232/I
3006 atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
> color (#!232 & sel) gray
> select clear
> select #232/A#232/E#234/A#234/E
3230 atoms, 3252 bonds, 410 residues, 2 models selected
> ui tool show "Color Actions"
> color sel khaki
[Repeated 4 time(s)]
> color sel peach puff
> color sel moccasin
[Repeated 1 time(s)]
> color sel khaki
[Repeated 4 time(s)]
> select #232/B#232/F#234/B#234/F
2640 atoms, 2652 bonds, 346 residues, 2 models selected
> color sel khaki
[Repeated 1 time(s)]
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> color sel plum
[Repeated 2 time(s)]
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> color sel plum
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume copy #3
Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
size 440,440,440, pixel 0.95, shown at step 1, values float32
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!43 models
> hide #!42 models
> hide #!44 models
> show #!44 models
> hide #!232 models
> show #!232 models
> ui tool show "Color Zone"
> hide #!44 models
> show #!44 models
> color zone #44 near #232 distance 5.7
> hide #!232 models
> lighting soft
> show #!42 models
> lighting soft
> lighting full
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!43 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color sel hot pink
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #43/I
Alignment identifier is 43/I
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> cartoon hide (#!43 & sel)
> lighting simple
> lighting soft
> show #!8 models
> color #8 #d6d6d6ff models
> color #8 #ebebebff models
> color #8 #ebebeb80 models
> color #8 silver models
[Repeated 1 time(s)]
> color #8 #c0c0c080 models
> color #8 #c0c0c08b models
> color #8 #c0c0c09e models
> color #8 #c0c0c0f5 models
> color #8 #c0c0c0f1 models
> color #8 #c0c0c0ad models
> color #8 #c0c0c0a1 models
> color #8 #c0c0c0ab models
> color #8 #c0c0c0ad models
> color #8 #c0c0c0b4 models
> color #8 #c0c0c0b6 models
> color #8 #c0c0c0b9 models
> color #8 #c0c0c0bd models
> color #8 #c0c0c0c1 models
> color #8 #c0c0c0bf models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #43/I:641
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:641-642
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:649
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #43/I:649-650
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #43/I:630
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:630-631
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:621
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:621-622
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I
6057 atoms, 6171 bonds, 2 pseudobonds, 745 residues, 2 models selected
> color sel slate blue
[Repeated 1 time(s)]
> color sel medium slate blue
> color sel slate blue
[Repeated 6 time(s)]
> color sel medium slate blue
> color sel medium orchid
> color sel dark orchid
> color sel magenta
> color sel dark slate blue
> color sel slate blue
> color sel violet
> color sel slate blue
> color sel medium slate blue
[Repeated 1 time(s)]
> select clear
> select #43/I:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> color sel light coral
> show #!8 models
> hide #!8 models
> select clear
> select #43/I:613-657
362 atoms, 362 bonds, 45 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616,618-619
31 atoms, 29 bonds, 3 residues, 1 model selected
> select #43/I:616,618-619,621-622
49 atoms, 46 bonds, 5 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 49 atom styles
> color sel dodger blue
> color sel royal blue
> color sel deep sky blue
> style sel ball
Changed 49 atom styles
> style sel sphere
Changed 49 atom styles
> style sel stick
Changed 49 atom styles
> style sel ball
Changed 49 atom styles
> select clear
> select #43/I:616,618-619,621-622,629
57 atoms, 53 bonds, 6 residues, 1 model selected
> select #43/I:616,618-619,621-622,629
57 atoms, 53 bonds, 6 residues, 1 model selected
> select
> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
4271 atoms, 4319 bonds, 523 residues, 1 model selected
> select clear
> select
> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
4271 atoms, 4319 bonds, 523 residues, 1 model selected
> select clear
> select #43/I:629
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:629
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:629,635-637
35 atoms, 33 bonds, 4 residues, 1 model selected
> select #43/I:629,635-637,640
43 atoms, 40 bonds, 5 residues, 1 model selected
> select #43/I:629,635-637,640,642-643
60 atoms, 56 bonds, 7 residues, 1 model selected
> select #43/I:629,635-637,640,642-643,646
68 atoms, 63 bonds, 8 residues, 1 model selected
> show sel target ab
> color sel crimson
> style sel ball
Changed 68 atom styles
> select clear
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!8 models
> hide #!8 models
> show #!8 models
> color #8 #00fdffff models
> color #8 #73fdffff models
> color #8 #009193ff models
> color #8 #00fdffff models
> color #8 #76d6ffff models
> color #8 #00fdffff models
> color #8 #76d6ffff models
> color #8 #76d6ffd2 models
> color #8 #76d6ff85 models
> color #8 #76d6ff86 models
> color #8 #76d6ffa6 models
> color #8 #76d6ff80 models
> lighting full
> hide #!8 models
> show #!8 models
> hide #!8 models
> lighting soft
> lighting full
> lighting soft
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
> supersample 6 width 2000 transparentBackground true
> lighting full
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
> supersample 6 width 2000 transparentBackground true
> hide #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
> supersample 6 width 2000 transparentBackground true
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
> supersample 6 width 2000 transparentBackground true
> hide #!42 models
> hide #!44 models
> show #!8 models
> color #8 #76d6ffff models
> lighting soft
> lighting full
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
> supersample 6 width 2000 transparentBackground true
> ui tool show "Hide Dust"
> surface dust #8 size 5.7
> surface dust #8 size 5.94
> surface dust #8 size 8.07
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
> supersample 6 width 2000 transparentBackground true
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
588,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
> hide #!8 models
> volume #45 step 1
> show #!8 models
> lighting simple
> select add #8
2 models selected
> view sel
> select subtract #8
Nothing selected
> hide #!8 models
> show #!42 models
> show #!44 models
> show #!43 models
> lighting soft
> lighting full
> lighting soft
> lighting full
> hide #!44 models
> hide #!43 models
> hide #!42 models
> show #!45 models
> hide #!45 models
> show #!8 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
> up_single_map.png supersample 6 width 2000 transparentBackground true
> hide #!8 models
> show #!42 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
> up_composite_map.png supersample 6 width 2000 transparentBackground true
> hide #!44 models
> hide #!43 models
> hide #!42 models
> show #!44 models
> show #!232 models
> hide #!232 models
> show #!232 models
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> ui mousemode right "rotate selected models"
> select subtract #232
Nothing selected
> select add #232
12124 atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
> view matrix models
> #232,-0.029351,-0.99871,0.041463,192.22,-0.84724,0.046867,0.52914,242.8,-0.5304,-0.019599,-0.84752,167.58
> view matrix models
> #232,-0.020898,-0.996,0.086876,194.54,-0.84044,0.064565,0.53805,243.54,-0.54151,-0.06177,-0.83842,167.34
> view matrix models
> #232,-0.042506,-0.99356,0.10504,195.69,-0.86935,0.088592,0.48619,241.57,-0.49236,-0.070649,-0.86752,165.27
> view matrix models
> #232,-0.053907,-0.99204,0.11378,196.27,-0.88276,0.1006,0.45894,240.51,-0.46673,-0.0757,-0.88115,164.26
> ui mousemode right "translate selected models"
> view matrix models
> #232,-0.053907,-0.99204,0.11378,197.1,-0.88276,0.1006,0.45894,241.87,-0.46673,-0.0757,-0.88115,162.33
> view matrix models
> #232,-0.053907,-0.99204,0.11378,197.14,-0.88276,0.1006,0.45894,241.9,-0.46673,-0.0757,-0.88115,162.25
> select subtract #232
Nothing selected
> hide #!44 models
> show #!44 models
> fitmap #232 inMap #44
Fit molecule 1id3 (#232) to map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) using 12124
atoms
average map value = 0.2847, steps = 68
shifted from previous position = 3.51
rotated from previous position = 4.37 degrees
atoms outside contour = 5383, contour level = 0.25
Position of 1id3 (#232) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
Matrix rotation and translation
-0.03410625 -0.99613821 0.08090390 194.35377785
-0.72343655 0.08045913 0.68568644 250.18361614
-0.68954791 -0.03514264 -0.72338695 177.33095720
Axis -0.66146232 0.70699818 0.25024222
Axis point 246.51764404 0.00000000 -9.19791182
Rotation angle (degrees) 146.98385179
Shift along axis 92.69735224
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!177 models
> hide #!177 models
> show #!232 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Wed Sep 4 08:32:44 2024 \u2014\u2014\u2014
opened ChimeraX session
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1328_map_sharp_zflip.mrc
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.0365, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #46 step 1
> volume #46 level 0.1209
> volume #46 level 0.27
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #46 inMap #44
Fit map cryosparc_P17_J1328_map_sharp_zflip.mrc in map
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy using 183011 points
correlation = 0.9983, correlation about mean = 0.9843, overlap = 3.392e+04
steps = 136, shift = 8.18, angle = 15.4 degrees
Position of cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) relative to
cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
Matrix rotation and translation
0.99999993 0.00020825 0.00029549 -0.11547030
-0.00020819 0.99999995 -0.00022028 0.08133560
-0.00029553 0.00022022 0.99999993 0.01845130
Axis 0.52030825 0.69808953 -0.49188447
Axis point 41.74969574 0.00000000 368.99527237
Rotation angle (degrees) 0.02425404
Shift along axis -0.01237652
> ui tool show "Hide Dust"
> surface dust #46 size 5.7
> surface dust #46 size 5.88
> surface dust #46 size 7.58
> surface undust #46
> surface dust #46 size 7.58
> show #!234 models
> hide #!234 models
> hide #!232 models
> show #!42 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1293_003_volume_map.mrc
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.131, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #47 step 1
> volume #47 level 0.2274
> select add #47
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #47,1,0,0,34.934,0,1,0,115.11,0,0,1,-196.72
> ui mousemode right "rotate selected models"
> view matrix models
> #47,0.80862,0.53112,-0.25306,75.22,-0.548,0.52343,-0.65247,630.75,-0.21408,0.66628,0.71431,-166.12
> view matrix models
> #47,-0.052033,0.59696,-0.80058,521.42,-0.88318,-0.4017,-0.24213,761.94,-0.46614,0.69446,0.54813,-35.04
> view matrix models
> #47,-0.56463,0.51635,-0.64387,621.88,-0.70577,-0.70651,0.052329,660.64,-0.42788,0.48397,0.76334,-85.832
> view matrix models
> #47,-0.64839,0.75691,-0.081716,371.53,-0.75724,-0.63011,0.17189,611.51,0.078617,0.17333,0.98172,-248.96
> view matrix models
> #47,-0.77683,0.61612,-0.13012,457.28,-0.62893,-0.76938,0.11179,628.86,-0.031234,0.16868,0.98518,-218.23
> view matrix models
> #47,0.12044,0.50172,0.8566,-162.62,-0.47586,-0.72811,0.49337,425.68,0.87123,-0.46705,0.15105,-7.2804
> view matrix models
> #47,0.92809,0.13752,0.34603,-111.13,-0.079004,-0.83541,0.54392,316.34,0.36388,-0.53214,-0.76447,512.58
> view matrix models
> #47,0.95173,-0.049595,-0.3029,179.09,0.060764,-0.93688,0.34433,377.51,-0.30086,-0.34611,-0.88865,710
> view matrix models
> #47,0.74227,-0.056059,-0.66775,384.14,0.082804,-0.98118,0.17442,448.01,-0.66497,-0.18476,-0.72366,713.19
> view matrix models
> #47,0.70283,0.024432,-0.71094,395.12,0.12328,-0.98847,0.0879,472.34,-0.7006,-0.14942,-0.69774,705.44
> view matrix models
> #47,0.054631,-0.15566,-0.9863,726.27,-0.030531,-0.98757,0.15417,489.48,-0.99804,0.02169,-0.058704,500.1
> view matrix models
> #47,0.60463,-0.27385,-0.74795,501.6,0.099908,-0.90554,0.41232,332.8,-0.79021,-0.32403,-0.52016,698.05
> view matrix models
> #47,0.52044,-0.22451,-0.82386,544.88,0.38474,-0.79968,0.46097,210.17,-0.76231,-0.55688,-0.32981,664.82
> ui mousemode right "translate selected models"
> color #47.1 light gray
> view matrix models
> #47,0.52044,-0.22451,-0.82386,558.57,0.38474,-0.79968,0.46097,110.43,-0.76231,-0.55688,-0.32981,702.7
> view matrix models
> #47,0.52044,-0.22451,-0.82386,437.12,0.38474,-0.79968,0.46097,87.569,-0.76231,-0.55688,-0.32981,677.12
> ui mousemode right "rotate selected models"
> view matrix models
> #47,0.56523,-0.45015,-0.69129,420.43,0.27696,-0.6858,0.67303,9.7394,-0.77705,-0.57187,-0.26296,658.06
> ui mousemode right "translate selected models"
> view matrix models
> #47,0.56523,-0.45015,-0.69129,423.1,0.27696,-0.6858,0.67303,13.1,-0.77705,-0.57187,-0.26296,647.01
> hide #!8 models
> show #!8 models
> fitmap #47 inMap #8
Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
correlation = 0.9671, correlation about mean = 0.6025, overlap = 1.762e+04
steps = 160, shift = 4.19, angle = 15.7 degrees
Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99987281 0.00432290 0.01535233 -6.92417661
-0.00420416 0.99996106 -0.00775858 5.37169883
-0.01538527 0.00769307 0.99985205 1.46498711
Axis 0.43594765 0.86722038 -0.24057941
Axis point 110.65380262 0.00000000 488.49257940
Rotation angle (degrees) 1.01544392
Shift along axis 1.28742242
> select subtract #47
Nothing selected
> hide #!46 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> color #16 #009193ff models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!8 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> fitmap #47 inMap #8
Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
correlation = 0.9671, correlation about mean = 0.6024, overlap = 1.762e+04
steps = 48, shift = 0.0108, angle = 0.0117 degrees
Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99987335 0.00426622 0.01533290 -6.90697298
-0.00414464 0.99995979 -0.00795249 5.42282003
-0.01536621 0.00788795 0.99985082 1.41490067
Axis 0.44553022 0.86344648 -0.23656498
Axis point 106.89545515 -0.00000000 488.26292061
Rotation angle (degrees) 1.01860486
Shift along axis 1.27033373
> hide #!8 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!42 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!46 models
> show #!46 models
> fitmap #44 inMap #46
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
steps = 40, shift = 0.00361, angle = 0.00695 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
0.99999996 -0.00014217 -0.00023873 0.08639737
0.00014220 0.99999998 0.00013580 -0.05048921
0.00023872 -0.00013583 0.99999996 -0.02306461
Axis -0.43914796 -0.77188188 0.45972540
Axis point 78.23841730 0.00000000 344.27567005
Rotation angle (degrees) 0.01772022
Shift along axis -0.00957291
> fitmap #44 inMap #46
Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
steps = 40, shift = 0.000257, angle = 0.000437 degrees
Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
0.99999996 -0.00014232 -0.00024540 0.08755876
0.00014235 0.99999998 0.00013952 -0.05131539
0.00024538 -0.00013955 0.99999996 -0.02371294
Axis -0.44137314 -0.77620112 0.45022392
Axis point 79.27979005 0.00000000 339.72277629
Rotation angle (degrees) 0.01811329
Shift along axis -0.00949115
> hide #!44 models
> show #!44 models
> hide #!46 models
> show #!46 models
> hide #!44 models
> show #!232 models
> show #!234 models
> hide #!232 models
> fitmap #234 inMap #46
Fit molecule copy of 1id3 (#234) to map
cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) using 6114 atoms
average map value = 0.2627, steps = 48
shifted from previous position = 0.184
rotated from previous position = 0.919 degrees
atoms outside contour = 3238, contour level = 0.27
Position of copy of 1id3 (#234) relative to
cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
Matrix rotation and translation
-0.04201562 -0.99848675 0.03548092 191.85732882
-0.66725181 0.05447399 0.74283754 251.20982793
-0.74364623 0.00753607 -0.66853085 181.90203052
Axis -0.65572927 0.69481226 0.29538966
Axis point 247.93591832 0.00000000 -19.62380013
Rotation angle (degrees) 145.89753760
Shift along axis 102.46918037
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!232 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> matchmaker #232/A to #234/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 1id3, chain A (#234) with 1id3, chain A (#232), sequence
alignment score = 617.3
RMSD between 97 pruned atom pairs is 0.000 angstroms; (across all 97 pairs:
0.000)
> hide #!234 models
> show #!234 models
> hide #!46 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!234 models
> ui mousemode right zoom
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel light goldenrod yellow
> color sel light yellow
[Repeated 15 time(s)]
> color sel light goldenrod yellow
[Repeated 1 time(s)]
> color sel yellow
[Repeated 10 time(s)]
> color sel yellow green
[Repeated 16 time(s)]
> color sel lime
> color sel yellow green
[Repeated 7 time(s)]
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> select #232/D#232/H#234/D#234/H
2976 atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
> color sel red
> color sel dark red
> color sel crimson
> color sel orange red
> color sel red
[Repeated 1 time(s)]
> color sel crimson
[Repeated 1 time(s)]
> color sel fire brick
[Repeated 4 time(s)]
> select #232/C#232/G#234/C#234/G
3382 atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
> color sel gold
[Repeated 3 time(s)]
> color sel dark orange
> color sel gold
[Repeated 4 time(s)]
> select #232/A#232/E#234/A#234/E
3230 atoms, 3252 bonds, 410 residues, 2 models selected
> color sel dodger blue
> color sel dark blue
> color sel medium blue
> color sel blue
[Repeated 1 time(s)]
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel cyan
> color sel deep sky blue
> color sel light sky blue
[Repeated 2 time(s)]
> color sel sky blue
[Repeated 1 time(s)]
> color sel light steel blue
[Repeated 4 time(s)]
> color sel powder blue
> color sel light steel blue
[Repeated 11 time(s)]
> color sel slate gray
> color sel light slate gray
> color sel cadet blue
> color sel steel blue
[Repeated 5 time(s)]
> color sel blue
[Repeated 3 time(s)]
> color sel medium blue
> color sel blue
[Repeated 3 time(s)]
> color sel dodger blue
> color sel steel blue
[Repeated 4 time(s)]
> select #232/B#232/F#234/B#234/F
2640 atoms, 2652 bonds, 346 residues, 2 models selected
> color sel medium aquamarine
> color sel dark cyan
> color sel medium aquamarine
[Repeated 1 time(s)]
> color sel dark cyan
> color sel turquoise
> color sel medium sea green
[Repeated 2 time(s)]
> color sel sea green
[Repeated 1 time(s)]
> color sel medium sea green
[Repeated 1 time(s)]
> color sel forest green
> color sel medium sea green
[Repeated 1 time(s)]
> color sel forest green
> color sel medium sea green
[Repeated 3 time(s)]
> select clear
> show #!235 models
> hide #!235 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> color #47 #d3d3d381 models
> color #47 #d6d6d6ff models
> color #47 silver models
> color #47 #c0c0c082 models
> color #47 #c0c0c0c8 models
> color #47 #c0c0c0c5 models
> color #47 #c0c0c0c1 models
> color #47 #c0c0c0be models
> color #47 #c0c0c0c2 models
> color #47 #c0c0c0c1 models
> color #47 #c0c0c0be models
> color #47 #c0c0c0c0 models
> color #47 #c0c0c0bf models
> hide #!232 models
> show #!232 models
> hide #!47 models
> hide #!42 models
> show #!42 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> hide #!47 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!232 models
> show #!232 models
> hide #!42 models
> show #!42 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!41 models
> hide #!41 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!1 models
> show #!1 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> show #!177 models
> hide #!177 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!22 models
> hide #!22 models
> show #!177 models
> hide #!177 models
> show #!177 models
> show #!232 models
> hide #!232 models
> hide #!177 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #1/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
alignment score = 5308.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> show #!38 models
> hide #!1 models
> show #!1 models
> hide #!38 models
> show #!40 models
> hide #!40 models
> combine #1
> hide #!48 models
> show #!48 models
> hide #!1 models
> hide #!48 models
> show #!48 models
> select #48/X,Y
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> select ~sel & ##selected
69387 atoms, 70556 bonds, 77 pseudobonds, 8899 residues, 3 models selected
> delete atoms (#!48 & sel)
> delete bonds (#!48 & sel)
> hide #!48 models
> show #!48 models
> rename #48 DNA_8xgc
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> select #48/X
1041 atoms, 1159 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel black
> select #48/Y
796 atoms, 894 bonds, 39 residues, 1 model selected
> color sel gray
> color sel dark gray
> color sel dim gray
> select clear
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!40 models
> show #!40 models
> hide #!48 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!40 models
> show #!40 models
> hide #!48 models
> hide #!40 models
> show #!8 models
> hide #!8 models
> show #!19 models
> hide #!19 models
> show #!42 models
> show #!48 models
> fitmap #48 inMap #42
Fit molecule DNA_8xgc (#48) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
copy (#42) using 1837 atoms
average map value = 0.2869, steps = 136
shifted from previous position = 2.41
rotated from previous position = 2.94 degrees
atoms outside contour = 1074, contour level = 0.3
Position of DNA_8xgc (#48) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
Matrix rotation and translation
0.97626723 0.21196039 0.04444217 20.25889577
0.20777495 -0.97457455 0.08386920 422.39463428
0.06108915 -0.07264478 -0.99548524 498.45034022
Axis -0.99403982 -0.10572708 -0.02658227
Axis point 0.00000000 219.96323566 240.74169709
Rotation angle (degrees) 175.48464775
Shift along axis -78.04663897
> hide #!48 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
> show #!234 models
> hide #!234 models
> show #!232 models
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
[Repeated 3 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> show #!234 models
> hide #!232 models
> hide #!42 models
> show #!41 models
> select #41/G
6693 atoms, 6778 bonds, 2 pseudobonds, 422 residues, 2 models selected
> select #41/H,G,F
20221 atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
> select
> #1/F#1/G#1/H#22/F#22/G#22/H#37/F#37/G#37/H#41/F#41/G#41/H#177/F#177/G#177/H
81053 atoms, 82328 bonds, 30 pseudobonds, 6355 residues, 10 models selected
> color sel royal blue
[Repeated 2 time(s)]
> color sel slate gray
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> color sel light sky blue
> color sel light blue
> color sel powder blue
> color sel deep sky blue
[Repeated 2 time(s)]
> color sel cyan
> color sel deep sky blue
[Repeated 2 time(s)]
> color sel dark turquoise
> color sel deep sky blue
> color sel steel blue
> color sel royal blue
> color sel dodger blue
> color sel deep sky blue
[Repeated 8 time(s)]
> select #1/I#22/I#38/X#41/X#43/I#177/X
51141 atoms, 51789 bonds, 27 pseudobonds, 4230 residues, 12 models selected
> color sel medium slate blue
[Repeated 1 time(s)]
> color sel slate blue
> color sel medium slate blue
> color sel medium orchid
> color sel dark slate blue
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
> color sel indigo
> color sel medium purple
[Repeated 4 time(s)]
> color sel medium slate blue
> color sel medium purple
> color sel medium slate blue
[Repeated 1 time(s)]
> color sel slate blue
> color sel medium slate blue
[Repeated 5 time(s)]
> select clear
> combine #1
> hide #!49 models
> show #!49 models
> select #49/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select ~sel & ##selected
65035 atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
> delete atoms (#!49 & sel)
> delete bonds (#!49 & sel)
> rename #49 N-term-Mcm2_8xgc
> select add #49
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color sel hot pink
> select clear
> matchmaker #49/2 to #23/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker N-Mcm2_6skl, chain 2 (#23) with N-term-Mcm2_8xgc, chain 2 (#49),
sequence alignment score = 3482.9
RMSD between 276 pruned atom pairs is 0.698 angstroms; (across all 293 pairs:
0.967)
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #49/2
Alignment identifier is 49/2
> select #49/2:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #49/2:126-152
214 atoms, 215 bonds, 27 residues, 1 model selected
> select ~sel & ##selected
5975 atoms, 6074 bonds, 5 pseudobonds, 753 residues, 3 models selected
> delete atoms (#!49 & sel)
> delete bonds (#!49 & sel)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 16:21:36 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #!48 models
> hide #!48 models
> hide #!49 models
> show #!49 models
> rename #49 N-patch-Mcm2_8xgc
> show #!43 models
> hide #!43 models
> show #!43 models
> ui tool show Matchmaker
> matchmaker #43/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
sequence alignment score = 5320.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> matchmaker #43/I to #38/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
sequence alignment score = 5320.2
RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
0.839)
> hide #!49 models
> hide #!43 models
> hide #!41 models
> show #!178 models
> hide #!178 models
> open /Users/cvetkom/Documents/cryoSPARC/J842_005_volume_map_EMReady.mrc
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 0.116, step 4, values float32
> volume #50 level 3.037
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #50 step 1
> volume #50 level 2.102
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!9 models
> hide #!9 models
> show #!47 models
> hide #!50 models
> show #!50 models
> show #!42 models
> select add #50
2 models selected
> lighting simple
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #50,1,0,0,-65.632,0,1,0,-229.59,0,0,1,71.364
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.4343,-0.44532,0.78299,-22.581,0.48395,0.84849,0.21414,-387.73,-0.75972,0.28593,0.58401,330.58
> ui mousemode right "move picked models"
> view matrix models
> #50,0.4343,-0.44532,0.78299,26.602,0.48395,0.84849,0.21414,-312.09,-0.75972,0.28593,0.58401,140.59
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-144.45,0.53432,0.73727,-0.41346,-106.79,-0.57506,0.67555,0.46146,19.955
> ui mousemode right "translate selected models"
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-121.97,0.53432,0.73727,-0.41346,-120.25,-0.57506,0.67555,0.46146,29.342
> view matrix models
> #50,0.61953,-0.0088021,0.78493,-138.14,0.53432,0.73727,-0.41346,-168.26,-0.57506,0.67555,0.46146,-2.6429
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.59893,-0.097848,0.7948,-111.13,0.56367,0.7565,-0.33163,-206.33,-0.56881,0.64663,0.50825,-10.607
> ui mousemode right zoom
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> select add #47
4 models selected
> select subtract #47
2 models selected
> hide #!47 models
> show #!47 models
> select subtract #50
Nothing selected
> select add #50
2 models selected
> select subtract #50
Nothing selected
> hide #!50 models
> show #!50 models
> hide #!42 models
> show #!42 models
> fitmap #50 inMap #42
Fit map J842_005_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map_sharp.mrc copy using 773474 points
correlation = 0.9586, correlation about mean = 0.8187, overlap = 1.895e+06
steps = 176, shift = 18.3, angle = 13 degrees
Position of J842_005_volume_map_EMReady.mrc (#50) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 0.00008926 0.00001426 -0.02716721
-0.00008926 1.00000000 0.00004509 0.03060850
-0.00001425 -0.00004509 1.00000000 0.00885891
Axis -0.44634943 0.14111659 -0.88366187
Axis point 329.25912566 261.27343201 0.00000000
Rotation angle (degrees) 0.00578781
Shift along axis 0.00861716
> hide #!42 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> volume #47 level 0.3135
> volume #47 level 0.3842
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> volume #47 level 0.3043
> volume #47 level 0.2735
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!46 models
> ui mousemode right "map eraser"
> hide #!47 models
> show #!47 models
> hide #!50 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_2.cxs
> volume erase #47 center 193.29,217.64,214.85 radius 57.536
Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #!52 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!46 models
> show #!42 models
> hide #!42 models
> show #!50 models
> hide #!52 models
> show #!52 models
> close #52
> show #!49 models
> hide #!49 models
> show #!49 models
> hide #!49 models
> show #!47 models
> hide #!46 models
> hide #!50 models
> volume erase #47 center 179.18,226.56,216.65 radius 57.536
Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
588,588,588, pixel 0.95, shown at step 1, values float32
> hide #51 models
> show #!46 models
> volume add #46,52
Opened volume sum as #53, grid size 1018,965,865, pixel 0.95, shown at step 1,
values float32
> volume #53 level 0.3701
> volume #53 level 0.4202
> volume #53 level 0.4569
> volume #53 level 0.5103
> select add #53
2 models selected
> close #53
> show #51 models
> hide #51 models
> show #!50 models
> show #!48 models
> hide #!48 models
> hide #!234 models
> show #!47 models
> volume add #47,50
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at step 1,
values float32
> volume #53 level 0.3458
> volume #53 level 0.4721
> volume #53 level 0.3819
> volume #53 level 0.2374
> volume #53 level 0.2555
[Repeated 1 time(s)]
> show #!47 models
> hide #!47 models
> show #!46 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> show #!232 models
> hide #!234 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> close #45,236
> show #!235 models
> close #235
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!178 models
> hide #!178 models
> close #178-179
> show #!52 models
> hide #!52 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> show #!46 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> show #!46 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> close #44
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> close #16-21
> show #!15 models
> hide #!15 models
> show #!15 models
> close #15
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> close #12
> show #!14 models
> hide #!14 models
> hide #!46 models
> hide #!53 models
> hide #!232 models
> show #!234 models
> hide #!234 models
> show #!232 models
> color #13 #b2ffff7e models
> color #13 #b2ffffb3 models
> color #13 #b2ffffc2 models
> close #23-40
> show #!22 models
> close #22
> show #!1 models
> hide #!1 models
> show #2 models
> select add #2
24908 atoms, 25142 bonds, 1555 residues, 1 model selected
> close #2
> show #!11 models
> hide #!11 models
> close #11
> show #!10 models
> close #10
> show #!9 models
> hide #!9 models
> close #9
> show #!8 models
> show #!7 models
> hide #!8 models
> close #7
> show #!6 models
> close #6
> show #!5 models
> close #5
> show #!4 models
> close #4
> show #!8 models
> hide #!8 models
> show #!3 models
> close #3
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!234 models
> show #!234 models
> hide #!232 models
> rename #234 histones
> show #!233 models
> hide #!234 models
> show #!46 models
> hide #!233 models
> show #!233 models
> hide #!13 models
> hide #!233 models
> show #!233 models
> hide #!46 models
> show #!46 models
> hide #!233 models
> show #!233 models
> hide #!46 models
> color #233 #b2b2b27c models
> show #!232 models
> color #233 #b2b2b27d models
> show #!41 models
> hide #!41 models
> show #!14 models
> hide #!233 models
> hide #!14 models
> show #!13 models
> close #14
> show #!8 models
> hide #!13 models
> hide #!8 models
> rename #1 Zhai
> show #!8 models
> rename #8 consensus_extended.mrc
> show #!13 models
> hide #!8 models
> rename #13 "deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z
> flip"
> show #!41 models
> hide #!13 models
> hide #!41 models
> show #!41 models
> rename #41 fitted_replisome
> show #!42 models
> hide #!41 models
> rename #42 "sharpened_replisome.mrc copy"
> show #!43 models
> hide #!42 models
> hide #!232 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> show #!233 models
> hide #!46 models
> show #!13 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!232 models
> show #!232 models
> hide #!233 models
> hide #!232 models
> show #!232 models
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!233 models
> show #!41 models
> hide #!41 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> show #!46 models
> rename #233 hetero_ref_good_nucleosome.mrc
> hide #!232 models
> show #!232 models
> rename #232 full_nucleosome
> show #!177 models
> hide #!232 models
> hide #!233 models
> rename #177 Baretic
> show #!53 models
> hide #!177 models
> show #!52 models
> hide #!53 models
> hide #!52 models
> show #!52 models
> hide #!52 models
> show #!52 models
> hide #!46 models
> hide #!43 models
> hide #!13 models
> rename #52 bad_nucleosome
> show #!50 models
> volume add #47,50
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at step 1,
values float32
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!53 models
> hide #!52 models
> close #51
> show #!50 models
> hide #!2 models
> show #!49 models
> hide #!50 models
> ui mousemode right zoom
> close #3
> show #!41 models
> combine #41 #49
Remapping chain ID '2' in N-patch-Mcm2_8xgc #49 to 'AD'
> close #41
> close #49
> hide #!3 models
> show #!3 models
> rename #3 full_replisome
> show #!2 models
> hide #!2 models
> show #!2 models
> close #4
> show #!233 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> color #233 #b2b2b2ff models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #!233 models
> show #!2 models
> show #!232 models
> combine #232
> rename #4 trimmed_nucleosome
> hide #!2 models
> select #13
2 models selected
> view sel
> select #232/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #232/I
Alignment identifier is 232/I
> sequence chain #232/J
Alignment identifier is 232/J
> select #232/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #232/I:1-21
422 atoms, 472 bonds, 21 residues, 1 model selected
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> delete atoms sel
> delete bonds sel
> select #232/J:292
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #232/J:255-292
786 atoms, 882 bonds, 38 residues, 1 model selected
> hide #!232 models
> hide #!4 models
> show #!4 models
> rename #4 full_nucleosome
> rename #232 trimmed_nucleosome
> show #!232 models
> hide #!4 models
> combine #232/I,J
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show #232/I,J
> undo
> select ~sel & ##selected
10916 atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
> select ~sel & ##selected
786 atoms, 882 bonds, 38 residues, 1 model selected
> select ~sel & ##selected
10916 atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
> select #232/I,J
5588 atoms, 6235 bonds, 185 pseudobonds, 301 residues, 3 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel ball
Changed 5588 atom styles
> select #232/J:162
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #232/J:162
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #232/J:147-162
318 atoms, 355 bonds, 16 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> close #5
> show #!4 models
> hide #!4 models
> undo
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> undo
[Repeated 5 time(s)]
> close #232
> show #!4 models
> combine #4
> rename #5 trimmedfull_nucleosome
> rename #5 trimmed_nucleosome
> show #!13 models
> select #4/I,J
6010 atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 6010 atom styles
> select clear
> select #4/I:20@O4
1 atom, 1 residue, 1 model selected
> select clear
> select #4/I:20@C7
1 atom, 1 residue, 1 model selected
> select add #4/J:274@O2
2 atoms, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #5/I
Alignment identifier is 5/I
> sequence chain #5/J
Alignment identifier is 5/J
> hide #!4 models
> select #5/I,J
6010 atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
> show sel atoms
> style sel ball
Changed 6010 atom styles
> select #5/I:20@C7
1 atom, 1 residue, 1 model selected
> select add #5/J:274@C7
2 atoms, 2 residues, 1 model selected
> select #5/J:274
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/J:274-292
394 atoms, 441 bonds, 19 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/I:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:1-21
422 atoms, 472 bonds, 21 residues, 1 model selected
> select #5/I:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:1-20
402 atoms, 450 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 white models
> color #2 #ffffff83 models
> color #2 #ffffff82 models
> show #!48 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #48
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 1837 atom styles
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #48/X:25
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #5/I:93
41 atoms, 44 bonds, 2 residues, 2 models selected
> select add #48/X:14
61 atoms, 65 bonds, 3 residues, 2 models selected
> select add #48/Y:37
81 atoms, 86 bonds, 4 residues, 2 models selected
> select add #48/Y:48
102 atoms, 109 bonds, 5 residues, 2 models selected
> combine #48
> rename #6 Zhai_DNA_trimmed
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/X
Alignment identifier is 6/X
> sequence chain #6/Y
Alignment identifier is 6/Y
> rename #6 Zhai_DNA
> rename #48 Zhai_DNA_trimmed
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #48/X
Alignment identifier is 48/X
> sequence chain #48/Y
Alignment identifier is 48/Y
> select #48/X:14
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/X:14-25
245 atoms, 273 bonds, 12 residues, 1 model selected
> select #48/X:13
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #48/X:9-13
103 atoms, 115 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/X:26
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/X:26-59
693 atoms, 769 bonds, 34 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/Y:32
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #48/Y:15-32
365 atoms, 410 bonds, 18 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #48/Y:49
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/Y:49-53
102 atoms, 113 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!6 models
> ui tool show "Fit in Map"
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #48 inMap #2
Fit molecule Zhai_DNA_trimmed (#48) to map volume sum (#2) using 574 atoms
average map value = 4.031, steps = 592
shifted from previous position = 14.2
rotated from previous position = 167 degrees
atoms outside contour = 5, contour level = 0.27354
Position of Zhai_DNA_trimmed (#48) relative to volume sum (#2) coordinates:
Matrix rotation and translation
-0.91975243 -0.27575503 0.27931101 510.33728112
-0.23429189 -0.18521113 -0.95436061 602.17741898
0.31490125 -0.94321578 0.10574123 368.51075021
Axis 0.19984288 -0.63818439 0.74349412
Axis point 200.04559281 464.04730525 0.00000000
Rotation angle (degrees) 178.40215888
Shift along axis -8.32738387
> volume #52 level 0.3197
> volume #2 level 0.9596
> volume #2 level 1.05
> hide #!2 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #48/X to #1/6 pairing ss
Match chain (Zhai_DNA_trimmed (#48) chain X) not compatible with BLOSUM-62
similarity matrix
> close #48
> show #!6 models
> combine #6
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
118294 atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
> select add #5
129622 atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #2 near #3 distance 2.68
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #5
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> color zone #2 near sel distance 2.68
[Repeated 1 time(s)]
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!52 models
> hide #!13 models
> select subtract #5
2 models selected
> select add #5
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
> select subtract #2
11328 atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
> select add #3
129622 atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
> color zone #2 near sel distance 2.68
> hide #!5 models
> hide #!3 models
> volume #233 level 2.785
> volume #2 level 1.357
> volume #2 level 0.8512
> volume #2 level 0.4721
> volume #2 level 0.3096
> color zone #2 near sel distance 5
> color zone #2 near sel distance 3
> color zone #2 near sel distance 3.5
> color zone #2 near sel distance 4
[Repeated 1 time(s)]
> volume splitbyzone #2
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 1 as #9.2, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 2 as #9.3, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 3 as #9.4, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 4 as #9.5, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 5 as #9.6, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 6 as #9.7, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 7 as #9.8, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 8 as #9.9, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32
Opened volume sum 9 as #9.10, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 10 as #9.11, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 11 as #9.12, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 12 as #9.13, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 13 as #9.14, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 14 as #9.15, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 15 as #9.16, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 16 as #9.17, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
Opened volume sum 17 as #9.18, grid size 636,840,859, pixel 0.95, shown at
level 0.31, step 1, values float32
> close #9.2-18
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!9.1 models
> hide #!9 models
> select #6/X:25
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #6/Y:37@C3'
22 atoms, 23 bonds, 2 residues, 1 model selected
> select add #6/Y:38
41 atoms, 43 bonds, 3 residues, 1 model selected
> select subtract #6/Y:37
40 atoms, 43 bonds, 2 residues, 1 model selected
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/X
Alignment identifier is 6/X
> sequence chain #6/Y
Alignment identifier is 6/Y
> select #6/X:26
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/X:26-59
693 atoms, 769 bonds, 34 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/Y:34
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #6/Y:34-53
411 atoms, 461 bonds, 20 residues, 1 model selected
> select #6/Y:36
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:36-53
370 atoms, 415 bonds, 18 residues, 1 model selected
> select #6/Y:39
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/Y:39-53
310 atoms, 348 bonds, 15 residues, 1 model selected
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!7 models
> select #6/Y:38
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #6/Y:15-38
486 atoms, 545 bonds, 24 residues, 1 model selected
> hide #!3 models
> select #6/Y:36
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:15-36
447 atoms, 502 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!9.1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #6/X:15
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #6/X:14
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/X:13
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/X:9-13
103 atoms, 115 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/Y:53
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/Y:49-53
102 atoms, 113 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show "Fit in Map"
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> fitmap #6 inMap #9.1
Fit molecule Zhai_DNA (#6) to map volume sum 0 (#9.1) using 492 atoms
average map value = 2.428, steps = 112
shifted from previous position = 2.38
rotated from previous position = 20.2 degrees
atoms outside contour = 57, contour level = 0.30965
Position of Zhai_DNA (#6) relative to volume sum 0 (#9.1) coordinates:
Matrix rotation and translation
0.84252921 0.47835125 0.24763810 -39.97421560
-0.52899667 0.64815172 0.54777905 144.67789487
0.10152374 -0.59251958 0.79913296 198.24507755
Axis -0.74601377 0.09559191 -0.65903387
Axis point 0.00000000 273.04359310 -103.91847500
Rotation angle (degrees) 49.84130149
Shift along axis -86.99886895
> show #!3 models
> show #!5 models
> select #5/I
2604 atoms, 2903 bonds, 3 pseudobonds, 142 residues, 2 models selected
> color (#!5 & sel) black
> select #5/J
2610 atoms, 2912 bonds, 5 pseudobonds, 141 residues, 2 models selected
> color (#!5 & sel) dim gray
> select clear
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select add #3
118294 atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!9.1 models
> hide #!9 models
> show #!2 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> combine #3 #6 #5
Remapping chain ID 'X' in Zhai_DNA #6 to 'Z'
Remapping chain ID 'Y' in Zhai_DNA #6 to 'a'
Remapping chain ID 'A' in trimmed_nucleosome #5 to 'K'
Remapping chain ID 'B' in trimmed_nucleosome #5 to 'L'
Remapping chain ID 'C' in trimmed_nucleosome #5 to 'M'
Remapping chain ID 'D' in trimmed_nucleosome #5 to 'N'
Remapping chain ID 'E' in trimmed_nucleosome #5 to 'O'
Remapping chain ID 'F' in trimmed_nucleosome #5 to 'P'
Remapping chain ID 'G' in trimmed_nucleosome #5 to 'Q'
Remapping chain ID 'H' in trimmed_nucleosome #5 to 'R'
Remapping chain ID 'I' in trimmed_nucleosome #5 to 'S'
Remapping chain ID 'J' in trimmed_nucleosome #5 to 'T'
> hide #!10 models
> show #!10 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!2 models
> close #6-7
> rename #10 extended_structure
> hide #!10 models
> show #!10 models
> select add #10
130114 atoms, 131991 bonds, 312 pseudobonds, 8456 residues, 4 models selected
> color zone #2 near sel distance 4.25
> color zone #2 near sel distance 53.56
[Repeated 1 time(s)]
> select clear
> volume #2 level 0.1833
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!13 models
> hide #!10 models
> hide #!2 models
Drag select of 6 atoms, 7 residues, 5 bonds
Drag select of 1 atoms, 4 residues, 1 bonds
Drag select of 48 atoms, 44 residues, 38 bonds
Drag select of 66 atoms, 50 residues, 55 bonds
> select #43/X,Y
1837 atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #43/I:606
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #43/I:657
13 atoms, 11 bonds, 2 residues, 1 model selected
> hide #!3 models
> select clear
Drag select of 35 atoms, 28 residues, 30 bonds
Drag select of 14 atoms, 18 residues, 11 bonds
Drag select of 8 residues
> select ~sel & ##selected
11865 atoms, 12085 bonds, 7 pseudobonds, 1480 residues, 3 models selected
> cartoon hide (#!43 & sel)
> cartoon (#!43 & sel)
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #43/I
Alignment identifier is 43/I
> select #43/I:605-606
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:11-606
4587 atoms, 4671 bonds, 2 pseudobonds, 570 residues, 2 models selected
> cartoon hide (#!43 & sel)
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
> select #43/I:658
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:658-781
1061 atoms, 1089 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #43
6598 atoms, 6698 bonds, 5 pseudobonds, 831 residues, 3 models selected
> select #43/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> delete atoms (#!43 & sel)
> delete bonds (#!43 & sel)
Drag select of 78 atoms, 55 residues, 65 bonds
> color sel red
> combine #43,3
Remapping chain ID 'I' in full_replisome #3 to 'K'
> hide #!6 models
> show #!6 models
> close #3
> rename #6 full_replisome
> combine #5,6
Remapping chain ID 'A' in full_replisome #6 to 'L'
Remapping chain ID 'B' in full_replisome #6 to 'M'
Remapping chain ID 'C' in full_replisome #6 to 'N'
Remapping chain ID 'D' in full_replisome #6 to 'O'
Remapping chain ID 'E' in full_replisome #6 to 'P'
Remapping chain ID 'F' in full_replisome #6 to 'Q'
Remapping chain ID 'G' in full_replisome #6 to 'R'
Remapping chain ID 'H' in full_replisome #6 to 'S'
Remapping chain ID 'I' in full_replisome #6 to 'T'
Remapping chain ID 'J' in full_replisome #6 to 'U'
> close #10
> rename #3 extended_structure
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 19:04:03 2024 \u2014\u2014\u2014
opened ChimeraX session
> open /Users/cvetkom/Desktop/extended_structure_old.pdb
Chain information for extended_structure_old.pdb #7
---
Chain | Description
0 7 | No description available
2 5 AD | No description available
3 6 | No description available
4 9 | No description available
8 AB | No description available
A | No description available
AA AC | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F G H | No description available
I | No description available
J | No description available
K O | No description available
L P | No description available
M Q | No description available
N R | No description available
S T | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> matchmaker #7/2 to #3/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#3) with extended_structure_old.pdb,
chain 2 (#7), sequence alignment score = 3554.3
RMSD between 293 pruned atom pairs is 0.000 angstroms; (across all 293 pairs:
0.000)
> select #7/a,Z
492 atoms, 550 bonds, 24 residues, 1 model selected
> select ~sel & ##selected
129622 atoms, 131441 bonds, 58 pseudobonds, 8432 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/a
247 atoms, 277 bonds, 12 residues, 1 model selected
> color sel dim gray
> select #7/Z
245 atoms, 273 bonds, 12 residues, 1 model selected
> color sel black
> combine #3,7
> hide #!10 models
> show #!10 models
> hide #!3 models
> hide #!7 models
> close #3,7
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!43 models
> hide #!6 models
> hide #!10 models
> show #!10 models
> rename #10 extended_structure
> select #10,T
Expected an objects specifier or a keyword
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
[Repeated 2 time(s)]
> select clear
> show #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> select add #10
130523 atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
> ui tool show "Color Zone"
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 10
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 15
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 20
[Repeated 1 time(s)]
> select clear
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> volume splitbyzone #2
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32
> volume #3.4 level 0.2577
> volume #3.4 level 0.1585
> volume #3.5 level 0.2148
> volume #3.4 level 0.183
> volume #3.5 level 0.183
> volume #3.9 level 0.9634
> volume #3.9 level 2.784
> volume #3.10 level 2.78
> volume #3.11 level 2.78
> volume #3.13 level 2.78
> volume #3.14 level 2.78
> volume #3.16 level 2.78
> volume #3.17 level 2.78
> volume #3.18 level 2.78
> volume #3.15 level 2.78
> volume #3.12 level 2.78
> volume copy #3.8
Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> volume #3.8 level 2.78
> volume #7 color #7b68ee7c
> volume #7 color #7b68ee33
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #!7 models
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> color zone #7 near sel distance 5.7
> show #!7 models
> volume #7 color #ff2600
> ui tool show "Color Actions"
> color sel medium slate blue
> select #7
2 models selected
> color sel medium slate blue
> volume #7 color #ff260081
> color sel medium slate blue
> select #10/T
409 atoms, 409 bonds, 51 residues, 1 model selected
> color sel purple
> color sel magenta
> color zone #7 near sel distance 5.7
> volume splitbyzone #7
Opened volume sum 7 copy 0 as #11.1, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32
> close #11.1
> show #!7 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!5 models
> select add #5
11737 atoms, 12370 bonds, 187 pseudobonds, 1146 residues, 4 models selected
> color zone #13 near sel distance 5.7
> color zone #13 near sel distance 6.18
> color zone #13 near sel distance 11.5
> select clear
> ui tool show "Hide Dust"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #3.3 size 5.7
> surface dust #3.3 size 5.66
> surface dust #3.3 size 33
> surface dust #3.3 size 33.37
> surface dust #3.3 size 14.12
> save
> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Fri Sep 6 19:48:00 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!11.2 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> rename #7 Tof1_lower_level
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> rename #11 Tof1_HTH_lower_level
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show "Hide Dust"
> hide #!13 models
> show #!13 models
> hide #!11 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> surface dust #13 size 5.7
[Repeated 1 time(s)]
> surface undust #13
> surface dust #13 size 5.7
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> show #!3.1 models
> hide #!3.1 models
> surface dust #3.2 size 5.7
> surface dust #3.2 size 5.68
> surface dust #3.2 size 13.68
> surface undust #3.2
> surface dust #3.2 size 13.68
> surface dust #3.2 size 14.86
[Repeated 1 time(s)]
> surface dust #3.4 size 5.7
> surface dust #3.3 size 14.12
> surface dust #3.3 size 14.38
> surface dust #3.3 size 6.94
> hide #!3.3 models
> show #!3.3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.8 models
> hide #!3.9 models
> hide #!3.10 models
> hide #!3.11 models
> hide #!3.12 models
> hide #!3.13 models
> hide #!3.14 models
> hide #!3.15 models
> hide #!3.16 models
> hide #!3.17 models
> hide #!3.18 models
> hide #!13 models
> surface dust #3.3 size 13.23
> surface undust #3.3
> surface dust #3.3 size 13.23
> ui tool show "Map Eraser"
> volume erase #3.3 center 191.19,155.01,168.45 radius 10.807
> show #!3.2 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> show #!3.8 models
> show #!3.9 models
> show #!3.10 models
> show #!3.11 models
> show #!3.12 models
> show #!3.13 models
> show #!3.14 models
> show #!3.15 models
> show #!3.16 models
> show #!3.17 models
> show #!3.18 models
> show #!5 models
> hide #!5 models
> show #!13 models
> hide #!13 models
> show #!13 models
> surface dust #3.4 size 5.7
> surface undust #3.4
> surface dust #3.4 size 7.66
> surface dust #3.5 size 5.7
> surface dust #3.5 size 6.18
> surface dust #3.5 size 8.89
> surface dust #3.6 size 5.7
> surface dust #3.6 size 5.97
> surface dust #3.6 size 6.94
> surface dust #3.8 size 7.05
> surface dust #3.8 size 7.54
> surface dust #3.8 size 5.15
> surface dust #3.7 size 5.7
> surface undust #3.9
> surface dust #3.9 size 5.7
> surface undust #3.8
> surface dust #3.8 size 5.15
> surface dust #3.9 size 5.7
> hide #!3.5 models
> show #!3.5 models
> surface undust #3.5
> surface dust #3.5 size 8.89
> lighting soft
> hide #!3 models
> show #!3 models
> select add #3
37 models selected
> view sel
> select subtract #3
Nothing selected
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side.png
> supersample 6 width 2000 transparentBackground true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side_back.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> surface dust #7 size 5.7
> surface dust #7 size 6.07
> surface dust #7 size 11.59
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> surface dust #2 size 5.7
> surface dust #2 size 5.97
> surface dust #2 size 35.17
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!2 models
> show #!2 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!42 models
> hide #!2 models
> show #!2 models
> hide #!42 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near #10 distance 19.41
> color zone #2 near #10 distance 13.26
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 16
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 18
> color zone #2 near #10 distance 1
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 20
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!13 models
> hide #!10 models
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Side View"
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 22
> color zone #2 near #10 distance 2
> color zone #2 near #10 distance 24
> hide #!2 models
> hide #!13 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!10 models
> hide #!10 models
> show #!13 models
> show #!43 models
> hide #!43 models
> show #!10 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> show #!43 models
> hide #!10 models
> hide #!43 models
> show #!43 models
> hide #!3 models
> show #!3 models
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel magenta
> hide sel target a
> select subtract #43
Nothing selected
> hide #!43 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level.png
> supersample 6 width 2000 transparentBackground true
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level.png
> supersample 6 width 2000 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> show #!1 models
> hide #!3 models
> hide #!13 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> show #!13 models
> show #!43 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!43 models
> show #!43 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11 models
> show #!11 models
> show #!7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> color #7 #7b68ee80 models
> color #7 #7b68ee9e models
> color #7 #7b68eea0 models
> color #7 #7b68ee32 models
> color #7 #7b68ee29 models
> color #7 #7b68eeab models
> color #7 #7b68ee89 models
> color #7 #7b68ee8a models
> hide #!43 models
> show #!43 models
> hide #!43 models
> hide #!7 models
> show #!7 models
> show #!43 models
> lighting simple
> lighting full
> lighting soft
> hide #!43 models
> show #!43 models
> hide #!13 models
> show #!13 models
> hide #!7 models
> hide #!13 models
> hide #!3 models
> show #!3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> volume copy #3.2
Opened volume sum 1 copy as #12, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> rename #12 leading_strand_vol_3p2
> volume copy #3.3
Opened volume sum 2 copy as #14, grid size 636,840,859, pixel 0.95, shown at
step 1, values float32
> hide #!14 models
> show #!14 models
> rename #14 lagging_strand_vol_3p3
> hide #!14 models
> hide #!12 models
> show #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.2 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> surface dust #12 size 5.7
> surface dust #12 size 5.59
> surface dust #12 size 9.82
> surface dust #12 size 5.68
[Repeated 1 time(s)]
> surface undust #12
> surface dust #12 size 5.68
> surface dust #14 size 5.7
> surface dust #14 size 6.18
> surface dust #14 size 21.74
> surface dust #14 size 22.85
> surface dust #14 size 18.43
> surface dust #14 size 19.68
> surface dust #14 size 14.62
> hide #!12 models
> hide #!14 models
> show #!3.2 models
> show #!3.3 models
> surface undust #3.2
> surface dust #3.2 size 14.86
> hide #!3.3 models
> hide #!3.2 models
> show #!12 models
> show #!14 models
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!14 models
> hide #15 models
> show #15 models
> hide #!43 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #15 models
> show #15 models
> volume erase #12 center 219.68,211.59,243.35 radius 53.859
> show #!3 models
> show #!3.2 models
> show #!3.3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume erase #12 center 202.99,259.45,180.39 radius 53.859
> volume erase #12 center 157.95,181.67,182.6 radius 53.859
> volume erase #12 center 178.35,160.14,212.29 radius 53.859
> volume erase #12 center 206.83,165.32,136.53 radius 18.769
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume erase #14 center 196.99,177.22,211.99 radius 31.01
> volume erase #14 center 212.15,214.12,242.94 radius 40.802
> volume erase #14 center 208.55,248.81,191.88 radius 40.802
> volume erase #14 center 168.65,198.46,168.27 radius 40.802
> volume erase #14 center 172.72,159.07,188.6 radius 40.802
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!12 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3.2 models
> hide #!3.3 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!3 models
> show #!3 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!43 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> show #!1 models
> open 8XGC fromDatabase pdb format mmcif
8xgc title:
Structure of yeast replisome associated with FACT and histone hexamer,
Composite map [more info...]
Chain information for 8xgc #15
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
8 | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
9 | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
B | DNA replication complex GINS protein PSF2 |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
M | FACT complex subunit POB3 | POB3_YEAST 1-552
N R | Histone H3 | A0A6A5Q536_YEASX 1-136
O S | Histone H4 | H4_YEAST 1-103
P | Histone H2A.1 | H2A1_YEAST 1-132
Q | Histone H2B.2 | H2B2_YEAST 1-131
X | DNA (51-MER) |
Y | DNA (39-MER) |
Non-standard residues in 8xgc #15
---
ADP \u2014 adenosine-5'-diphosphate
ZN \u2014 zinc ion
> show #!177 models
> hide #!177 models
> ui tool show Matchmaker
> matchmaker #15/I to #1/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Zhai, chain I (#1) with 8xgc, chain I (#15), sequence alignment
score = 5609.4
RMSD between 745 pruned atom pairs is 0.000 angstroms; (across all 745 pairs:
0.000)
> select add #15
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> hide (#!15 & sel) target a
> cartoon (#!15 & sel)
> select subtract #15
Nothing selected
> select add #15
82765 atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
> select subtract #15
Nothing selected
> hide #!15 models
> select #1/N#1/R#15/N#15/R
2740 atoms, 2766 bonds, 334 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dodger blue
[Repeated 2 time(s)]
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel dodger blue
[Repeated 1 time(s)]
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel cyan
[Repeated 1 time(s)]
> color sel deep sky blue
> color sel dodger blue
> color sel steel blue
> color sel slate blue
> color sel royal blue
> color sel dodger blue
> select #1/O#1/S#15/O#15/S
2534 atoms, 2560 bonds, 316 residues, 2 models selected
> color sel medium spring green
> color sel medium aquamarine
> color sel sea green
> color sel medium sea green
> color sel light sea green
[Repeated 1 time(s)]
> color sel medium spring green
[Repeated 1 time(s)]
> select #1/P#15/P
1406 atoms, 1422 bonds, 182 residues, 2 models selected
> select #1/P#15/P
1406 atoms, 1422 bonds, 182 residues, 2 models selected
> color sel gold
[Repeated 1 time(s)]
> select #1/Q#15/Q
1412 atoms, 1432 bonds, 182 residues, 2 models selected
> color sel crimson
> select #1/L#15/L
6948 atoms, 7044 bonds, 6 pseudobonds, 986 residues, 4 models selected
> color sel salmon
[Repeated 2 time(s)]
> color sel tomato
> color sel salmon
> select #1/M#15/M
3752 atoms, 3736 bonds, 14 pseudobonds, 758 residues, 4 models selected
> color sel sienna
> color sel saddle brown
> color sel brown
[Repeated 1 time(s)]
> color sel tomato
> color sel fire brick
> color sel orange red
> color sel brown
> color sel sienna
> select clear
> lighting simple
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> color (#!1 & sel) hot pink
> hide #!1 models
> select add #1
71224 atoms, 72609 bonds, 163 pseudobonds, 8989 residues, 4 models selected
> select subtract #1
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #43/I
Alignment identifier is 43/I
> show #!1 models
> hide #!1 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> color #3.2 #00000081 models
> color #3.2 #0000009d models
> color #3.2 #00000099 models
> color #3.3 #696969a7 models
> color #3.3 #696969a0 models
> color #3.3 #6969699a models
> color #3.3 #69696999 models
> color #3.4 #4682b49a models
> color #3.4 #4682b499 models
> color #3.5 #3cb37193 models
> color #3.5 #3cb37199 models
> color #3.6 #ffd7009c models
> color #3.6 #ffd7009a models
> color #3.6 #ffd70099 models
> hide #!13 models
> show #!13 models
> color #13 #b2ffffbf models
[Repeated 1 time(s)]
> color #13 #b2ffffc5 models
> color #13 #b2ffffc4 models
> color #13 #b2ffffb0 models
> color #13 #b2ffff9f models
> color #13 #b2ffff9b models
> color #13 #b2ffff98 models
> color #13 #b2ffff99 models
> color zone #13 near #10 distance 5.7
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #3.7 #b222229c models
> color #3.7 #b222229b models
> color #3.7 #b2222297 models
> color #3.7 #b2222298 models
> color #3.7 #b2222299 models
> hide #!3.8 models
> show #!3.8 models
> show #!234 models
> hide #!234 models
> hide #!13 models
> show #!13 models
> color #13 #b2ffffff models
> show #!9 models
> hide #!9 models
> hide #!3.18 models
> show #!3.18 models
> hide #!3.17 models
> show #!3.17 models
> hide #!3.8 models
> show #!3.8 models
> color #3.7 firebrick models
> color #3.6 gold models
> color #3.5 mediumseagreen models
> color #3.4 steelblue models
> hide #!3.3 models
> show #!3.3 models
> color #3.3 dimgrey models
> color #3.2 black models
> hide #!13 models
> show #!13 models
> color zone #13 near #10 distance 5.7
[Repeated 1 time(s)]
> color zone #13 near #10 distance 5.87
> color zone #13 near #10 distance 12.76
> ui tool show "Side View"
> lighting soft
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> hide #!13 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!14 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #43/I:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:618-619
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #43/I:616
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616-617
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #43/I:609
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:609
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:609,616
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #43/I:609,616,618-619
40 atoms, 37 bonds, 4 residues, 1 model selected
> select #43/I:609,616,618-619,621-622
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:609,616,618-619,621-622,632
67 atoms, 62 bonds, 7 residues, 1 model selected
> select #43/I:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:616,632
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #43/I:616,618-619,632
40 atoms, 37 bonds, 4 residues, 1 model selected
> select #43/I:616,618-619,621-622,632
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:616,618-619,621-622,632
58 atoms, 54 bonds, 6 residues, 1 model selected
> select #43/I:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:619
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #43/I:616,619
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #43/I:616,618-619
31 atoms, 29 bonds, 3 residues, 1 model selected
> select #43/I:616,618-619,621-622
49 atoms, 46 bonds, 5 residues, 1 model selected
> show sel target ab
> color sel byhetero
[Repeated 1 time(s)]
> style sel sphere
Changed 49 atom styles
> hide #!12 models
> show #!12 models
> ui tool show "Color Actions"
> color sel cyan
[Repeated 2 time(s)]
> color sel byhetero
[Repeated 1 time(s)]
> select #43/I:616,618-619,621-622,635-636
67 atoms, 63 bonds, 7 residues, 1 model selected
> select #43/I:635
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/I:635-637
27 atoms, 26 bonds, 3 residues, 1 model selected
> select #43/I:627,635-637
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #43/I:627,629,635-637
44 atoms, 41 bonds, 5 residues, 1 model selected
> select #43/I:627,629,635-637,640
52 atoms, 48 bonds, 6 residues, 1 model selected
> select #43/I:627,629,635-637,640,642-643
69 atoms, 64 bonds, 8 residues, 1 model selected
> select #43/I:627,629,635-637,640,642-643,646
77 atoms, 71 bonds, 9 residues, 1 model selected
> color sel orange red
> show sel target ab
> color sel byhetero
> style sel ball
Changed 77 atom styles
> style sel sphere
Changed 77 atom styles
> color sel orange
> color sel orange red
> color sel gold
> color sel orange
> color sel byhetero
> select add #43
409 atoms, 409 bonds, 51 residues, 1 model selected
> select subtract #43
Nothing selected
> cartoon style #12,14,43#3.8-18#!3 xsection oval modeHelix default
> cartoon style #12,14,43#3.8-18#!3 xsection rectangle modeHelix default
> cartoon style (#12,14,43#3.8-18#!3 & coil) xsection oval
> cartoon style #12,14,43#3.8-18#!3 xsection barbell modeHelix default
> cartoon style #12,14,43#3.8-18#!3 modeHelix tube sides 20
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches.png
> supersample 6 width 2000 transparentBackground true
> show #!13 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> show #!3.5 models
> show #!3.6 models
> show #!3.7 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_2.png
> supersample 6 width 2000 transparentBackground true
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_3.png
> supersample 6 width 2000 transparentBackground true
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select #43/I:607-609
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> hide sel target a
> color sel magenta
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_lighter.png
> supersample 6 width 2000 transparentBackground true
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level_lighter.png
> supersample 6 width 2000 transparentBackground true
> hide #!2 models
> show #!3 models
> show #!7 models
> color #7 #7b68ee81 models
> color #7 #7b68ee80 models
> color #7 #7b68ee73 models
> color #7 #7b68ee41 models
> color #7 #7b68ee96 models
> color #7 #7b68ee8c models
> color #7 #7b68ee95 models
> color #7 #7b68ee9c models
> color #7 #7b68ee96 models
> color #7 #7b68ee99 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> color #11.2 #ff00ff83 models
> color #11.2 #ff00ff3b models
> color #11.2 #ff00ff4d models
> color #11.2 #ff00ff68 models
> color #11.2 #ff00ff77 models
> color #11.2 #ff00ff87 models
> color #11.2 #ff00ff9e models
> color #11.2 #ff00ff9a models
> hide #!11.2 models
> color #11.2 #ff00ff99 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> select #43/I:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I
409 atoms, 409 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> color sel blue violet
[Repeated 2 time(s)]
> color sel blue
> color sel dark blue
> color sel navy
[Repeated 2 time(s)]
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_transp.png
> supersample 6 width 2000 transparentBackground true
> select #43/I:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #43/I:607-656
402 atoms, 402 bonds, 50 residues, 1 model selected
> color sel magenta
> select clear
> color #11.2 #ff00ff3b models
> color #11.2 #ff00ff71 models
> color #11.2 magenta models
> color #11.2 white models
> color #11.2 #ffffff72 models
> color #11.2 #ffffff5f models
> color #11.2 #ffffff79 models
> color #11.2 #ffffff4d models
> color #11.2 #ffffff5e models
> color #11.2 #ff40ffff models
> select clear
[Repeated 1 time(s)]
> hide #!11.2 models
> hide #!11 models
> hide #!43 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_flat.png
> supersample 6 width 2000 transparentBackground true
> lighting soft
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_background.png
> supersample 6 width 2000 transparentBackground true
> show #!43 models
> show #!1 models
> hide #!3 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #3.2 black models
> color #3.3 dimgrey models
> color #3.4 steelblue models
> color #3.5 mediumseagreen models
> color #3.6 #ffd700fd models
> color #3.6 gold models
> color #3.7 firebrick models
> hide #!3 models
> show #!3 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> select #1/L,M
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon hide (#!1 & sel)
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
> supersample 6 width 2000 transparentBackground true
> select add #12
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
> select add #14
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 6 models selected
> select subtract #14
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
> select subtract #12
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon (#!1 & sel)
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_with_FACT.png
> supersample 6 width 2000 transparentBackground true
> show #!12 models
> show #!14 models
> hide #!13 models
> hide #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai.png
> supersample 6 width 2000 transparentBackground true
> select #1/L,M
5350 atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
> cartoon hide (#!1 & sel)
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
> supersample 6 width 2000 transparentBackground true
> hide #!12 models
> hide #!14 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!3.7 models
> show #!3.6 models
> show #!3.5 models
> show #!3.4 models
> show #!3.3 models
> show #!3.2 models
> show #!13 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT_wo_nucl.png
> supersample 6 width 2000 transparentBackground true
> cartoon (#!1 & sel)
> select clear
> hide #!1 models
> show #!43 models
> combine #1
> select #16/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select ~sel & ##selected
65035 atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
> show #!7 models
> hide #!7 models
> show #!11 models
> show #!11.2 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!11 models
> hide #!11 models
> show #!11 models
> color #11.2 #ff40ffde models
> color #11.2 #ff40ffce models
> color #11.2 #ff40ffcc models
> hide #!11.2 models
> show #!11.2 models
> hide #!11.2 models
> show #!11.2 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH_density.png
> supersample 6 width 2000 transparentBackground true
> hide #!11 models
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH.png
> supersample 6 width 2000 transparentBackground true
> show #!1 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Mon Sep 9 04:24:31 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!16 models
> show #!16 models
> hide #!1 models
> hide #!16 models
> show #!16 models
> show #!1 models
> combine #1
> hide #!1 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!3 models
> hide #!13 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!17 models
> show #!17 models
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #17/Q to #10/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain D (#10) with copy of Zhai, chain Q (#17),
sequence alignment score = 586.9
RMSD between 88 pruned atom pairs is 0.795 angstroms; (across all 91 pairs:
1.028)
> hide #!10 models
> select #17/Q,P,O,N,S,R,L,M
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> select ~sel & ##selected
61828 atoms, 63129 bonds, 153 pseudobonds, 7610 residues, 4 models selected
> delete atoms (#!17 & sel)
> delete bonds (#!17 & sel)
> show #!8 models
> hide #!8 models
> show #!10 models
> select add #10
130523 atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
> view sel
> select subtract #10
Nothing selected
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> select clear
> select #17/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #17/L
Alignment identifier is 17/L
> select clear
> select #17/L:961-996
197 atoms, 197 bonds, 36 residues, 1 model selected
> select #17/L:956
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #17/L:948-956
65 atoms, 67 bonds, 9 residues, 1 model selected
> select #17/L:948-950
22 atoms, 23 bonds, 3 residues, 1 model selected
> select #17/L:948-996
262 atoms, 264 bonds, 1 pseudobond, 45 residues, 2 models selected
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!1 models
> hide #!1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!17 models
> hide #!43 models
> combine #15
> hide #!18 models
> select add #17
9396 atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
> select subtract #17
Nothing selected
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!1 models
> hide #!1 models
> combine #1
> select #19/Q,P,O,N,S,R,L,M,2
15585 atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
> select ~sel & ##selected
55639 atoms, 56840 bonds, 148 pseudobonds, 6830 residues, 4 models selected
> hide (#!19 & sel) target a
> hide #!19 models
> show #!19 models
> cartoon hide (#!19 & sel)
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!10 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!19 models
> hide #!16 models
> show #!16 models
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!16 models
> hide #!19 models
> show #!19 models
> cartoon (#!19 & sel)
> delete atoms (#!19 & sel)
> delete bonds (#!19 & sel)
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!17 models
> ui tool show Matchmaker
> matchmaker #19/L to #17/L pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of Zhai, chain L (#17) with copy of Zhai, chain L (#19),
sequence alignment score = 4482.1
RMSD between 493 pruned atom pairs is 0.000 angstroms; (across all 493 pairs:
0.000)
> hide #!19 models
> show #!19 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!10 models
> hide #!19 models
> show #!19 models
> select #19/L
3474 atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
> select #19/2
6189 atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
> select add #19
15585 atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
> select subtract #19
Nothing selected
> hide #!19 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
\u2014\u2014\u2014 End of log from Wed Sep 11 12:56:29 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> show #!10 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!50 models
> hide #!50 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_sharp.mrc
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map.mrc
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.108, step 4, values float32
> hide #!10 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> volume #20 step 1
> volume #20 level 0.6282
> volume #20 level 0.5581
> volume #21 step 1
> volume #21 level 0.3191
> show #!50 models
> hide #!20 models
> show #!10 models
> hide #!10 models
> show #!20 models
> select add #20
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.99684,0.061516,0.050168,-28.958,-0.064381,0.99626,0.057647,4.4916,-0.046434,-0.060695,0.99708,30.666
> lighting simple
> view matrix models
> #20,0.73598,-0.4705,-0.48679,329.31,0.6768,0.52918,0.51178,-191.97,0.01681,-0.70611,0.7079,265.3
> view matrix models
> #20,0.12559,-0.15204,-0.98036,539.99,-0.57343,0.79527,-0.1968,269.08,0.80957,0.58689,0.012694,-138.71
> view matrix models
> #20,-0.16726,-0.54653,-0.82057,691.05,-0.96595,-0.075783,0.24736,507.43,-0.19738,0.83401,-0.51525,212.61
> view matrix models
> #20,-0.44936,-0.35876,-0.81815,718.23,-0.88005,0.3352,0.33637,346.68,0.15357,0.87116,-0.46636,90.611
> view matrix models
> #20,-0.44063,-0.37463,-0.81578,719.55,-0.88716,0.32048,0.33201,353.87,0.13706,0.87003,-0.47357,97.439
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.44063,-0.37463,-0.81578,705.11,-0.88716,0.32048,0.33201,144.71,0.13706,0.87003,-0.47357,26.598
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.33684,-0.44475,-0.8299,698.78,-0.91245,0.37165,0.17118,178.84,0.2323,0.81491,-0.531,29.613
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.33684,-0.44475,-0.8299,696.83,-0.91245,0.37165,0.17118,160.27,0.2323,0.81491,-0.531,22.667
> ui tool show "Fit in Map"
> fitmap #20 inMap #50
Fit map cryosparc_P17_J819_005_volume_map_sharp.mrc in map
J842_005_volume_map_EMReady.mrc using 218333 points
correlation = 0.9383, correlation about mean = 0.6201, overlap = 1.633e+06
steps = 320, shift = 3.21, angle = 32.8 degrees
Position of cryosparc_P17_J819_005_volume_map_sharp.mrc (#20) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
-0.97651784 -0.21085655 -0.04418632 623.63633661
-0.20170911 0.96689998 -0.15626218 100.15142454
0.07567265 -0.14368002 -0.98672676 575.82401984
Axis 0.10410159 -0.99168284 0.07568362
Axis point 308.30489723 0.00000000 301.22875456
Rotation angle (degrees) 176.53538416
Shift along axis 9.18353169
> select subtract #20
Nothing selected
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> volume #20 level 0.55
> volume #20 level 0.52
> ui mousemode right zoom
> select add #20
2 models selected
> view sel
> select subtract #20
Nothing selected
> show #!10 models
> hide #!20 models
> show #!20 models
> volume #20 level 0.5
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui tool show "Color Zone"
> color zone #20 near #10 distance 5.7
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!20 models
> show #!20 models
> hide #!10 models
> show #!10 models
> hide #!20 models
> show #!20 models
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_13_mrc1_mcm265_cdc45/fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif
Chain information for fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> ui tool show Matchmaker
> matchmaker #22/B to #10/5 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 5 (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3612.5
RMSD between 349 pruned atom pairs is 0.656 angstroms; (across all 376 pairs:
1.211)
> select add #22
34895 atoms, 35428 bonds, 4406 residues, 1 model selected
> hide sel target a
> cartoon sel
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select subtract #22
Nothing selected
> show #!21 models
> hide #!21 models
> show #!21 models
> fitmap #21 inMap #50
Fit map cryosparc_P17_J819_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 385073 points
correlation = -0.002927, correlation about mean = 0.004409, overlap = -0.0752
steps = 684, shift = 150, angle = 30.2 degrees
Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.57579874 0.59202822 -0.56387799 140.55370059
0.23007257 0.54448263 0.80660106 227.62276282
0.78455237 -0.59417273 0.17730296 170.40181219
Axis -0.70827102 -0.68180470 -0.18301506
Axis point 0.00000000 142.99311800 40.24521085
Rotation angle (degrees) 81.44306259
Shift along axis -285.93048023
> hide #!20 models
> show #!20 models
> lighting simple
> select add #21
3 models selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.97135,-0.052031,-0.23188,161.6,0.15157,0.88715,0.43587,-376.59,0.18303,-0.45853,0.86962,210.47
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.19048,0.81338,-0.54967,226.48,0.29087,0.48802,0.82294,-405.4,0.93761,-0.31663,-0.14363,216.66
> view matrix models
> #21,-0.32552,0.21775,-0.92012,629.77,-0.85556,0.34648,0.38467,69.087,0.40256,0.91244,0.073519,-23.833
> view matrix models
> #21,-0.53454,-0.15623,-0.83058,768.38,-0.79246,0.43422,0.42833,16.109,0.29374,0.88715,-0.35592,123.32
> view matrix models
> #21,-0.53754,0.14132,-0.83131,687.98,-0.53102,0.70909,0.46391,-142.08,0.65503,0.69082,-0.30612,62.244
> view matrix models
> #21,-0.084069,-0.50373,-0.85976,743.6,-0.50818,0.76385,-0.39785,56.165,0.85714,0.40347,-0.3202,87.35
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.084069,-0.50373,-0.85976,600,-0.50818,0.76385,-0.39785,93.73,0.85714,0.40347,-0.3202,23.425
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.11912,-0.5728,-0.81099,616.38,-0.60623,0.68884,-0.39748,141.88,0.78632,0.44429,-0.4293,60.08
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.11912,-0.5728,-0.81099,641.5,-0.60623,0.68884,-0.39748,134.93,0.78632,0.44429,-0.4293,-49.603
> select subtract #21
Nothing selected
> fitmap #21 inMap #50
Fit map cryosparc_P17_J819_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 385073 points
correlation = 0.9655, correlation about mean = 0.736, overlap = 1.153e+06
steps = 428, shift = 23.7, angle = 35.9 degrees
Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
-0.97650910 -0.21085482 -0.04438713 623.66015597
-0.20170409 0.96695488 -0.15592857 100.07508728
0.07579864 -0.14331260 -0.98677052 575.69053694
Axis 0.10409896 -0.99169665 0.07550605
Axis point 308.29085690 0.00000000 301.17618213
Rotation angle (degrees) 176.52597465
Shift along axis 9.14636480
> ui mousemode right zoom
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!20 models
> color #21 #ffffb2b1 models
> color #21 #ffffb2c3 models
> color #21 #ffffb2cd models
> lighting soft
> hide #!21 models
> show #!20 models
> hide #!10 models
> hide #!20 models
> show #!21 models
> color #21 #ffffb2ff models
> volume #21 level 0.3
> show #!10 models
> hide #22 models
> hide #!21 models
> show #!21 models
> volume #21 color #ffffb2a7
> volume #21 color #ffffb2c7
> volume #21 level 0.2436
> lighting simple
> volume #21 level 0.1591
> show #22 models
> volume #21 level 0.1281
> volume #21 level 0.1788
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> select #22/1
Nothing selected
> hide #22 models
> show #22 models
> select #22/A
8735 atoms, 8850 bonds, 1096 residues, 1 model selected
> color sel red
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel fire brick
[Repeated 1 time(s)]
> select clear
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #22 models
> show #22 models
> hide #!21 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> matchmaker #22/E to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
alignment score = 3080.7
RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
1.017)
> show #!21 models
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> color #21 #ffffb2bd models
> color #21 #ffffb2b5 models
> color #21 #ffffb2b2 models
> color #21 #ffffb2b3 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!21 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map.mrc
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.12, step 4, values float32
> select add #23
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,-7.0847,0,1,0,-197.97,0,0,1,-109.28
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.98683,-0.1075,-0.12084,64.211,0.093694,0.98898,-0.11463,-186.41,0.13184,0.1018,0.98603,-171.46
> view matrix models
> #23,0.94591,0.31213,-0.088466,-59.663,-0.29926,0.73415,-0.60948,142.32,-0.12529,0.60298,0.78785,-193.05
> view matrix models
> #23,0.82112,-0.20887,0.53116,-52.333,0.43246,0.83502,-0.34017,-166.12,-0.37248,0.50903,0.77598,-94.238
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.82112,-0.20887,0.53116,-76.409,0.43246,0.83502,-0.34017,-186.01,-0.37248,0.50903,0.77598,-92.077
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.83793,-0.011709,0.54565,-144.2,0.24675,0.89989,-0.35961,-149.17,-0.48681,0.43596,0.75693,-33.526
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.83793,-0.011709,0.54565,-128.24,0.24675,0.89989,-0.35961,-146.49,-0.48681,0.43596,0.75693,-40.894
> fitmap #23 inMap #50
Fit map cryosparc_P17_J842_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 31738 points
correlation = 0.8988, correlation about mean = 0.8848, overlap = 2.616e+04
steps = 240, shift = 14.4, angle = 16.1 degrees
Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.99999950 -0.00093282 -0.00036048 0.38612693
0.00093288 0.99999955 0.00017577 -0.28600473
0.00036032 -0.00017611 0.99999992 -0.03720041
Axis -0.17327202 -0.35493124 0.91869507
Axis point 306.61813627 413.85199204 0.00000000
Rotation angle (degrees) 0.05817852
Shift along axis 0.00043119
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #23 step 1
> select subtract #23
Nothing selected
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> hide #!21 models
> volume #20 level 0.4302
> volume #20 level 0.3778
> volume #20 level 0.35
> color zone #20 near #10 distance 5.7
> color single #20
> color #20 #b2b2b2d5 models
> color #20 #b2b2b2be models
> color #20 #b2b2b2bf models
> hide #!10 models
> show #!10 models
> hide #22 models
> show #22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> fitmap #23 inMap #50
Fit map cryosparc_P17_J842_005_volume_map.mrc in map
J842_005_volume_map_EMReady.mrc using 2030930 points
correlation = 0.8962, correlation about mean = 0.8821, overlap = 1.677e+06
steps = 40, shift = 0.0507, angle = 0.0557 degrees
Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
1.00000000 -0.00007868 -0.00004863 0.03041624
0.00007868 0.99999998 -0.00016626 0.01451905
0.00004864 0.00016625 0.99999998 -0.05718112
Axis 0.87385342 -0.25564418 0.41355321
Axis point 0.00000000 342.00873970 86.09530376
Rotation angle (degrees) 0.01090079
Shift along axis -0.00077981
> volume #23 level 0.2075
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!23 models
> show #!21 models
> hide #!23 models
> hide #!21 models
> hide #22 models
> show #22 models
> select clear
> hide #22 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #22 models
> show #!20 models
> hide #!21 models
> volume #20 level 0.38
> volume #20 level 0.4
> volume #20 level 0.45
> show #22 models
> hide #22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #22 models
> hide #22 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> color #23 #b2ffffcc models
> show #22 models
> hide #22 models
> show #22 models
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #22 models
> show #22 models
> hide #22 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> ui mousemode right zoom
> hide #!23 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J1282_volume_map.mrc
Opened cryosparc_P17_J1282_volume_map.mrc as #24, grid size 588,588,588, pixel
0.95, shown at level 0.156, step 4, values float32
> close #24
> show #22 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #22 models
> show #22 models
> matchmaker #22/B to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3101.9
RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
7.919)
> matchmaker #22/C to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain C (#22), sequence
alignment score = 468.1
RMSD between 6 pruned atom pairs is 1.308 angstroms; (across all 25 pairs:
19.655)
> hide #22 models
> show #22 models
> matchmaker #22/B to #10/AD pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AD (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3101.9
RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
7.919)
> hide #!23 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> matchmaker #22/E to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
alignment score = 3080.7
RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
1.017)
> matchmaker #22/B to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
alignment score = 3481.1
RMSD between 244 pruned atom pairs is 0.690 angstroms; (across all 293 pairs:
3.338)
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> volume #23 level 0.18
> hide #22 models
> show #22 models
> hide #22 models
> show #!21 models
> show #22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> volume #21 level 0.16
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #22 models
> show #22 models
> hide #!21 models
> hide #!23 models
> hide #22 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif
Chain information for
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif #24
---
Chain | Description
A | .
B | .
C | .
D E | .
F G | .
H I J | .
K | .
> select add #24
34488 atoms, 35097 bonds, 4327 residues, 1 model selected
> hide sel target a
> cartoon sel
> select subtract #24
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #24/B to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain B
(#24), sequence alignment score = 3082.5
RMSD between 545 pruned atom pairs is 0.663 angstroms; (across all 564 pairs:
0.931)
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> matchmaker #24/C to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain C
(#24), sequence alignment score = 3488.9
RMSD between 245 pruned atom pairs is 0.669 angstroms; (across all 293 pairs:
1.945)
> select #24/A
1510 atoms, 1527 bonds, 185 residues, 1 model selected
> color sel red
> select #10/M:96
22 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> color #10,24 hot pink
> undo
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel hot pink
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> color sel blue violet
> color sel orchid
> color sel deep pink
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel medium violet red
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel magenta
> select clear
> select #24/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel dark orchid
> select clear
> show #22 models
> hide #22 models
> show #22 models
> hide #24 models
> hide #22 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #!10 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> select #24/D,E
2164 atoms, 2190 bonds, 272 residues, 1 model selected
> color sel dodger blue
> color sel steel blue
> color sel dodger blue
> select clear
> show #!10 models
> select #24/K
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> select clear
> select #24/K
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> color sel yellow green
> color sel orange
> select clear
[Repeated 1 time(s)]
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!10 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
Chain information for fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
#25
---
Chain | Description
A | .
B | .
C | .
D E F | .
G | .
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> select add #25
30722 atoms, 31289 bonds, 3849 residues, 1 model selected
> select subtract #25
Nothing selected
> select add #25
30722 atoms, 31289 bonds, 3849 residues, 1 model selected
> hide sel target a
> cartoon sel
> select subtract #25
Nothing selected
> matchmaker #25/B to #24/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
chain B (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
chain B (#25), sequence alignment score = 3315.9
RMSD between 585 pruned atom pairs is 0.430 angstroms; (across all 650 pairs:
3.003)
> hide #!10 models
> matchmaker #25/C to #24/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
chain C (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
chain C (#25), sequence alignment score = 4205.3
RMSD between 670 pruned atom pairs is 0.557 angstroms; (across all 868 pairs:
28.308)
> hide #24 models
> show #24 models
> hide #24 models
> select #25/A
1510 atoms, 1527 bonds, 185 residues, 1 model selected
> color sel red
> color sel orange red
> select clear
> show #24 models
> select #25/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> select #25/G
6063 atoms, 6153 bonds, 775 residues, 1 model selected
> color sel coral
> color sel sienna
> select clear
[Repeated 1 time(s)]
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #25 models
> select #24/H,I,J
10980 atoms, 11241 bonds, 1371 residues, 1 model selected
> color sel slate gray
> color sel cadet blue
> select add #24
34488 atoms, 35097 bonds, 4327 residues, 1 model selected
> select subtract #24
Nothing selected
> hide #24 models
> show #24 models
> hide #24 models
> show #25 models
> select #25/D,E,F
10980 atoms, 11241 bonds, 1371 residues, 1 model selected
> color sel medium aquamarine
> color sel cyan
> select clear
> show #24 models
> show #!10 models
> hide #25 models
> hide #24 models
> hide #!10 models
> show #24 models
> show #25 models
> hide #25 models
> show #25 models
> hide #24 models
> show #!10 models
> hide #!10 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> hide #24 models
> hide #25 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_323_337_tof1_model_0.cif
Chain information for fold_mrc1_323_337_tof1_model_0.cif #26
---
Chain | Description
A | .
B | .
> select #26/B
9945 atoms, 10133 bonds, 1238 residues, 1 model selected
> color sel slate blue
> color sel medium slate blue
[Repeated 4 time(s)]
> color sel dark slate blue
[Repeated 1 time(s)]
> color sel rebecca purple
[Repeated 4 time(s)]
> select clear
> show #!10 models
> matchmaker #26/B to #10/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain X (#10) with
fold_mrc1_323_337_tof1_model_0.cif, chain B (#26), sequence alignment score =
5350.8
RMSD between 514 pruned atom pairs is 0.989 angstroms; (across all 665 pairs:
3.879)
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif
Chain information for fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif #27
---
Chain | Description
A | .
B | .
C | .
D | .
> matchmaker #27/B to #10/X pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain X (#10) with
fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif, chain B (#27), sequence
alignment score = 5344.2
RMSD between 523 pruned atom pairs is 0.976 angstroms; (across all 665 pairs:
3.339)
> select #27/B
9945 atoms, 10133 bonds, 1238 residues, 1 model selected
> color sel blue violet
> select #27/A
201 atoms, 202 bonds, 24 residues, 1 model selected
> color sel red
> select #27/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> color sel orchid
> color sel medium orchid
[Repeated 1 time(s)]
> color sel dark orchid
> color sel medium orchid
> select clear
> select #27/D
7928 atoms, 8057 bonds, 1017 residues, 1 model selected
> color sel light coral
> select clear
> hide #26 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_385_456_mcm6_model_0.cif
Chain information for fold_mrc1_385_456_mcm6_model_0.cif #28
---
Chain | Description
A | .
B | .
> hide #27 models
> hide #28 models
> show #28 models
> select #28/A
560 atoms, 562 bonds, 72 residues, 1 model selected
> color sel red
> select clear
> matchmaker #28/B to #10/AB pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain AB (#10) with
fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
4104.2
RMSD between 300 pruned atom pairs is 0.858 angstroms; (across all 332 pairs:
2.385)
> hide #28 models
> show #28 models
> hide #!10 models
> show #!10 models
> matchmaker #28/B to #10/8 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 8 (#10) with
fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
4030.4
RMSD between 253 pruned atom pairs is 0.826 angstroms; (across all 305 pairs:
2.667)
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #28/A
560 atoms, 562 bonds, 72 residues, 1 model selected
> color sel dark red
> select #28/B
7928 atoms, 8057 bonds, 1017 residues, 1 model selected
> color sel orange
> select clear
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_813_865_mcm2_cdc45_model_0.cif
Chain information for fold_mrc1_813_865_mcm2_cdc45_model_0.cif #29
---
Chain | Description
A | .
B | .
C | .
> select #29/A
445 atoms, 451 bonds, 53 residues, 1 model selected
> color sel red
> select clear
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel pale violet red
> select clear
> matchmaker #29/B to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B (#29), sequence alignment
score = 13
Fewer than 3 residues aligned; cannot match extended_structure, chain 2 with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> select #29/C
6938 atoms, 7047 bonds, 868 residues, 1 model selected
> matchmaker #29/C to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain C (#29), sequence alignment
score = 3493.1
RMSD between 246 pruned atom pairs is 0.605 angstroms; (across all 293 pairs:
1.580)
> color sel pale violet red
> select #29/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel gray
[Repeated 5 time(s)]
> color sel light gray
> color sel gray
> color sel light yellow
[Repeated 1 time(s)]
> color sel old lace
[Repeated 1 time(s)]
> color sel antique white
[Repeated 1 time(s)]
> color sel ghost white
> color sel mint cream
> color sel white smoke
[Repeated 1 time(s)]
> color sel beige
[Repeated 1 time(s)]
> color sel azure
> color sel wheat
[Repeated 1 time(s)]
> select clear
> hide #28 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> open
> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_908_925_cdc45_model_0.cif
Chain information for fold_mrc1_908_925_cdc45_model_0.cif #30
---
Chain | Description
A | .
B | .
> select #30/B
5231 atoms, 5321 bonds, 650 residues, 1 model selected
> color sel lavender
> color sel gainsboro
> color sel dim gray
> color sel gray
> color sel light gray
> color sel thistle
[Repeated 1 time(s)]
> select #30/A
145 atoms, 146 bonds, 18 residues, 1 model selected
> color sel red
> select clear
> matchmaker #30/B to #10/P pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain P (#10) with
fold_mrc1_908_925_cdc45_model_0.cif, chain B (#30), sequence alignment score =
3073.5
RMSD between 536 pruned atom pairs is 0.657 angstroms; (across all 564 pairs:
1.134)
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Mon Sep 16 15:36:42 2024 \u2014\u2014\u2014
opened ChimeraX session
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif #31
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif #32
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif
Chain information for
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif #33
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> hide #30 models
> hide #32 models
> hide #33 models
> hide #31 models
> show #31 models
> ui tool show Matchmaker
> matchmaker #31/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif, chain A (#31),
sequence alignment score = 3496.1
RMSD between 253 pruned atom pairs is 0.662 angstroms; (across all 293 pairs:
1.847)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #31
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> show #32 models
> show #33 models
> select add #32
75104 atoms, 76324 bonds, 9428 residues, 2 models selected
> select add #33
112656 atoms, 114486 bonds, 14142 residues, 3 models selected
> hide sel target a
> cartoon sel
> select subtract #33
75104 atoms, 76324 bonds, 9428 residues, 2 models selected
> select subtract #32
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> select subtract #31
Nothing selected
> hide #32 models
> hide #33 models
> show #32 models
> show #33 models
> select #31/A #32/A #33/A
20814 atoms, 21141 bonds, 2604 residues, 3 models selected
> color sel hot pink
> select #31/B #32/B #33/B
7806 atoms, 7926 bonds, 1002 residues, 3 models selected
> color sel yellow
> select #31/C #32/C #33/C
23784 atoms, 24171 bonds, 3051 residues, 3 models selected
> color sel orange
> select #31/D #32/D #33/D
15693 atoms, 15963 bonds, 1950 residues, 3 models selected
> color sel light gray
> select #31/E #32/E #33/E
29835 atoms, 30399 bonds, 3714 residues, 3 models selected
> ui tool show "Color Actions"
> color sel slate blue
> select #31/F #32/F #33/F
14724 atoms, 14886 bonds, 1821 residues, 3 models selected
> color sel red
> select add #31
47368 atoms, 48086 bonds, 5928 residues, 3 models selected
> select add #32
80012 atoms, 81286 bonds, 10035 residues, 3 models selected
> select subtract #31
42460 atoms, 43124 bonds, 5321 residues, 2 models selected
> select subtract #32
4908 atoms, 4962 bonds, 607 residues, 1 model selected
> select add #33
37552 atoms, 38162 bonds, 4714 residues, 1 model selected
> select subtract #33
Nothing selected
> select clear
> matchmaker #32/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif, chain A (#32),
sequence alignment score = 3505.1
RMSD between 253 pruned atom pairs is 0.693 angstroms; (across all 293 pairs:
1.550)
> matchmaker #33/A to #10/2 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif, chain A (#33),
sequence alignment score = 3502.1
RMSD between 258 pruned atom pairs is 0.659 angstroms; (across all 293 pairs:
1.500)
> lighting simple
> hide #32 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #32 models
> hide #32 models
> show #32 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> show #32 models
> hide #32 models
> hide #!10 models
> show #!50 models
> hide #!50 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Tue Sep 24 13:00:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> lighting simple
> open /Users/cvetkom/Documents/pdb/4c95_Ctf4_Sld5.pdb
4c95_Ctf4_Sld5.pdb title:
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to SLD5
[more info...]
Chain information for 4c95_Ctf4_Sld5.pdb #34
---
Chain | Description
A B C | No description available
D E | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #34
9660 atoms, 9722 bonds, 4 pseudobonds, 1360 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #34
Nothing selected
> select #34/A
3494 atoms, 3493 bonds, 2 pseudobonds, 510 residues, 2 models selected
> select #34/B
3531 atoms, 3550 bonds, 1 pseudobond, 498 residues, 2 models selected
> select #34/C
2427 atoms, 2473 bonds, 1 pseudobond, 326 residues, 2 models selected
> select #34/D
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/E
104 atoms, 103 bonds, 13 residues, 1 model selected
> select #34/D,E
208 atoms, 206 bonds, 26 residues, 1 model selected
> color sel red
> hide #31 models
> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_3c_ctf4_mrc1_1081_1096/fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif
Chain information for fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif #35
---
Chain | Description
A B C | .
D | .
> show #!10 models
> hide #!23 models
> select clear
> ui tool show Matchmaker
> matchmaker #34/B to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with 4c95_Ctf4_Sld5.pdb, chain B
(#34), sequence alignment score = 2232.7
RMSD between 391 pruned atom pairs is 0.878 angstroms; (across all 424 pairs:
1.248)
> matchmaker #35/A to #10/S pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker extended_structure, chain S (#10) with
fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif, chain A (#35), sequence
alignment score = 2301.6
RMSD between 411 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.817)
> hide #!10 models
> show #!10 models
> show #!23 models
> hide #!23 models
> show #!42 models
> color #42 #b2b2ffeb models
> color #42 #b2b2ffff models
> color #42 #b2b2ffb7 models
> color #42 #b2b2ff95 models
> color #42 #b2b2ff84 models
> hide #!10 models
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> hide #!42 models
> show #!42 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #35 models
> show #35 models
> hide #!42 models
> show #!42 models
> hide #35 models
> show #35 models
> select #35/D
128 atoms, 129 bonds, 16 residues, 1 model selected
> color sel orange
> color sel orange red
> color sel orange
> select clear
> hide #!34 models
> show #!34 models
> ui tool show "Fit in Map"
> hide #!42 models
> show #!42 models
> fitmap #34 inMap #42
Fit molecule 4c95_Ctf4_Sld5.pdb (#34) to map sharpened_replisome.mrc copy
(#42) using 9660 atoms
average map value = 0.381, steps = 128
shifted from previous position = 2.63
rotated from previous position = 6.17 degrees
atoms outside contour = 4354, contour level = 0.3
Position of 4c95_Ctf4_Sld5.pdb (#34) relative to sharpened_replisome.mrc copy
(#42) coordinates:
Matrix rotation and translation
0.28572805 -0.31647925 0.90454429 338.42345045
-0.43402411 -0.88427381 -0.17228725 294.11719747
0.85439016 -0.34336673 -0.39002146 373.35631167
Axis -0.80114939 0.23486712 -0.55045172
Axis point 0.00000000 201.64420355 57.39058667
Rotation angle (degrees) 173.87077288
Shift along axis -407.56390486
> fitmap #35 inMap #42
Fit molecule fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) to map
sharpened_replisome.mrc copy (#42) using 11336 atoms
average map value = 0.4111, steps = 68
shifted from previous position = 0.628
rotated from previous position = 1.83 degrees
atoms outside contour = 4371, contour level = 0.3
Position of fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) relative
to sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
-0.98706242 -0.07882972 0.13961966 285.86123137
0.08488406 0.48183004 0.87214363 299.11678968
-0.13602378 0.87271169 -0.46890494 372.10103280
Axis 0.00177188 0.85978425 0.51065438
Axis point 149.35362784 0.00000000 83.84935178
Rotation angle (degrees) 170.77580491
Shift along axis 447.69744149
> hide #35 models
> hide #!42 models
> show #!42 models
> hide #!34 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> hide #!42 models
> show #!42 models
> color #42 #b2b2ffff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> show #!233 models
> hide #!233 models
> show #!233 models
> hide #!233 models
> show #!47 models
> show #!46 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> hide #!42 models
> hide #!46 models
> show #!43 models
> hide #!43 models
> show #!34 models
> show #33 models
> hide #33 models
> show #35 models
> hide #!34 models
> show #!34 models
> hide #35 models
> show #35 models
> show #!2 models
> hide #!2 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
\u2014\u2014\u2014 End of log from Wed Sep 25 19:02:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!34 models
> hide #35 models
> show #35 models
> hide #35 models
> close #2-3
> close #7
> close #11
> close #9
> show #!50 models
> hide #!50 models
> show #!53 models
> close #53
> show #!52 models
> close #52
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!10 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
\u2014\u2014\u2014 End of log from Fri Oct 4 13:17:26 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_EMready.mrc
Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
588,588,588, pixel 0.95, shown at level 0.0383, step 4, values float32
> volume #2 step 1
> volume #2 level 0.9283
> volume #2 level 1.647
> ui tool show "Side View"
> hide #!2 models
> show #!21 models
> show #!2 models
> select add #2
2 models selected
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.21372,0.65189,-0.72758,228.01,-0.15215,0.75791,0.63437,-52.313,0.96497,-0.024879,0.26116,-76.828
> view matrix models
> #2,-0.22904,0.42092,-0.8777,455.06,-0.48229,0.73415,0.47793,87.401,0.84554,0.53277,0.034859,-139.12
> view matrix models
> #2,-0.30253,0.24312,-0.92161,536.06,-0.68897,0.61238,0.38771,202.38,0.65863,0.75225,-0.017761,-133.46
> view matrix models
> #2,-0.17917,0.019523,-0.98362,578.75,-0.64564,0.75206,0.13253,216.8,0.74233,0.65881,-0.12214,-104.65
> view matrix models
> #2,-0.39996,0.21624,-0.89066,563.08,-0.18128,0.93391,0.30815,-9.3049,0.89843,0.28471,-0.33432,8.6733
> view matrix models
> #2,-0.45252,0.485,-0.74833,467.43,0.38691,0.86285,0.32525,-154.48,0.80345,-0.14235,-0.57811,215.56
> view matrix models
> #2,-0.19899,0.25008,-0.94756,511.54,0.14679,0.96359,0.22349,-88.484,0.96895,-0.094621,-0.22845,66.354
> view matrix models
> #2,-0.40366,0.20697,-0.89119,566.81,-0.0090314,0.97313,0.23009,-48.812,0.91486,0.10093,-0.39095,69.189
> view matrix models
> #2,-0.42359,0.12332,-0.89742,597.11,0.0008642,0.99074,0.13574,-32.363,0.90585,0.056721,-0.41978,91.291
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.42359,0.12332,-0.89742,572.5,0.0008642,0.99074,0.13574,-244.94,0.90585,0.056721,-0.41978,20.155
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.42268,0.11844,-0.8985,573.87,0.0011522,0.99149,0.13015,-243.8,0.90628,0.053978,-0.41923,20.651
> view matrix models
> #2,-0.54332,-0.16268,-0.82361,666.33,-0.42868,0.89727,0.10557,-90.185,0.72182,0.41043,-0.55725,9.6598
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,654.96,-0.41205,0.88859,0.20156,-117.01,0.6926,0.44919,-0.56439,9.0402
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,657.43,-0.41205,0.88859,0.20156,-126.64,0.6926,0.44919,-0.56439,12.296
> view matrix models
> #2,-0.59204,-0.092954,-0.80053,663.52,-0.41205,0.88859,0.20156,-124.44,0.6926,0.44919,-0.56439,2.3033
> ui mousemode right zoom
> ui tool show "Fit in Map"
> fitmap #2 inMap #21
Fit map cryosparc_P17_J819_005_volume_map_EMready.mrc in map
cryosparc_P17_J819_005_volume_map.mrc using 740829 points
correlation = 0.938, correlation about mean = 0.7691, overlap = 1.576e+06
steps = 160, shift = 3.85, angle = 10.8 degrees
Position of cryosparc_P17_J819_005_volume_map_EMready.mrc (#2) relative to
cryosparc_P17_J819_005_volume_map.mrc (#21) coordinates:
Matrix rotation and translation
0.99999999 0.00005310 -0.00009395 0.01216343
-0.00005312 0.99999998 -0.00020453 0.08100750
0.00009394 0.00020453 0.99999998 -0.07859161
Axis 0.88443714 -0.40622568 -0.22967726
Axis point 0.00000000 388.90207101 387.88928499
Rotation angle (degrees) 0.01324986
Shift along axis -0.00409883
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!20 models
> show #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
> volume #3 step 1
> volume #3 level 0.2175
> volume #3 level 0.4032
> select add #3
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96087,0.15628,0.2287,-100.29,-0.086083,0.95323,-0.28971,123.99,-0.26328,0.25869,0.92939,24.765
> view matrix models
> #3,0.94784,0.022072,0.31799,-87.222,0.026112,0.98887,-0.14647,39.853,-0.31769,0.14713,0.93671,67.954
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.94784,0.022072,0.31799,-188.13,0.026112,0.98887,-0.14647,-129.94,-0.31769,0.14713,0.93671,62.858
> view matrix models
> #3,0.94784,0.022072,0.31799,-118.63,0.026112,0.98887,-0.14647,-168.34,-0.31769,0.14713,0.93671,-44.135
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-179.94,0.1255,0.94252,-0.30967,-134.37,-0.59565,0.32121,0.73623,46.771
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.79338,0.092061,0.60172,-166.19,0.1255,0.94252,-0.30967,-142.23,-0.59565,0.32121,0.73623,35.37
> view matrix models
> #3,0.79338,0.092061,0.60172,-165.26,0.1255,0.94252,-0.30967,-141.13,-0.59565,0.32121,0.73623,35.671
> select subtract #3
Nothing selected
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 329084 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.568e+05
steps = 236, shift = 0.4, angle = 16.9 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 -0.00001351 0.00004557 -0.02152036
0.00001352 1.00000000 -0.00003397 0.01017840
-0.00004557 0.00003397 1.00000000 0.00711885
Axis 0.58150158 0.77996616 0.23131947
Axis point 171.08172050 0.00000000 434.91154679
Rotation angle (degrees) 0.00334730
Shift along axis -0.00292859
> hide #!42 models
> show #!42 models
> volume #3 level 0.3
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> ui mousemode right zoom
> ui tool show "Hide Dust"
> surface undust #42
> fitmap #3 inMap #42
Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 586182 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.874e+05
steps = 28, shift = 0.0238, angle = 0.00733 degrees
Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:
Matrix rotation and translation
1.00000000 0.00000906 -0.00005933 0.02130757
-0.00000906 1.00000000 0.00003559 -0.01782195
0.00005933 -0.00003559 1.00000000 0.00029158
Axis -0.51008916 -0.85026779 -0.12982191
Axis point -14.19118466 0.00000000 395.65343560
Rotation angle (degrees) 0.00399795
Shift along axis 0.00424682
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
480,480,480, pixel 0.95, shown at level 0.152, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.95, shown at level 0.28, step 2, values float32
> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc
Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
480,480,480, pixel 0.95, shown at level 0.569, step 2, values float32
> volume #11 level 2.423
> volume #9 level 0.9574
> volume #11 step 1
> volume #9 step 1
> volume #7 step 1
> volume #7 level 0.2399
> select add #7
2 models selected
> select add #9
4 models selected
> select add #11
6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#9,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#11,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2
> view matrix models
> #7,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#9,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#11,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885
> view matrix models
> #7,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#9,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#11,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14
> view matrix models
> #7,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#9,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#11,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79
> view matrix models
> #7,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#9,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#11,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21
> view matrix models
> #7,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#9,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#11,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05
> view matrix models
> #7,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#9,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#11,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39
> view matrix models
> #7,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#9,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#11,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06
> view matrix models
> #7,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#9,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#11,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57
> view matrix models
> #7,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#9,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#11,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6
> view matrix models
> #7,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#9,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#11,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#9,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#11,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#9,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#11,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2
> view matrix models
> #7,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#9,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#11,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#9,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#11,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52
> view matrix models
> #7,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#9,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#11,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#9,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#11,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51
> view matrix models
> #7,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#9,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#11,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95
> view matrix models
> #7,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#9,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#11,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87
> view matrix models
> #7,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#9,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#11,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3
> view matrix models
> #7,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#9,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#11,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!23 models
> hide #!23 models
> show #!23 models
> fitmap #7 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 611645 points
correlation = 0.8586, correlation about mean = 0.4556, overlap = 8.71e+04
steps = 244, shift = 17, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map.mrc (#7) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55644781 -0.77930109 0.28819374 245.87868586
-0.75685869 -0.33229301 0.56280215 362.24414012
-0.34282757 -0.53129197 -0.77472452 653.58997201
Axis -0.86611289 0.49953261 0.01776598
Axis point 0.00000000 386.34237031 252.82329186
Rotation angle (degrees) 140.83086649
Shift along axis -20.39427278
> hide #!7 models
> show #!7 models
> fitmap #9 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 166113 points
correlation = 0.8354, correlation about mean = 0.2023, overlap = 1.093e+05
steps = 240, shift = 17.3, angle = 22.5 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc (#9) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55535502 -0.78023657 0.28777020 246.41094031
-0.75768547 -0.33209636 0.56180488 362.67622759
-0.34277328 -0.53004046 -0.77560530 653.54700022
Axis -0.86582981 0.50001893 0.01788295
Axis point 0.00000000 386.54023823 252.88749245
Rotation angle (degrees) 140.91153143
Shift along axis -20.31760982
> fitmap #11 inMap #23
Fit map Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 547647 points
correlation = 0.755, correlation about mean = 0.2272, overlap = 1.157e+06
steps = 244, shift = 16, angle = 22.6 degrees
Position of Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc (#11) relative
to cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.55439930 -0.78039733 0.28917368 246.34842101
-0.75807382 -0.33013049 0.56243927 362.20292573
-0.34346106 -0.53103093 -0.77462290 653.67877730
Axis -0.86543769 0.50070495 0.01766816
Axis point 0.00000000 386.83809960 252.79416826
Rotation angle (degrees) 140.82108735
Shift along axis -20.29310612
> ui mousemode right zoom
> select subtract #7
4 models selected
> select subtract #9
2 models selected
> select subtract #11
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #9 level 0.7158
> volume #9 level 0.7
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.4
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!9 models
> show #!9 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #26 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #26 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!50 models
> hide #!9 models
> hide #!50 models
> show #!50 models
> color #50 #b2b2b29c models
> volume #50 level 3
> volume #50 level 3.5
> volume #50 level 3.6
> volume #50 level 3.8
> volume #50 level 4.5
> show #!42 models
> hide #!50 models
> hide #!42 models
> show #!3 models
> select add #3
2 models selected
> color #3.1 gray
> ui tool show "Color Actions"
> color sel light blue
> color sel light sky blue
[Repeated 4 time(s)]
> color sel aquamarine
> color sel light sky blue
> select subtract #3
Nothing selected
> color #3 #87cefaa8 models
> color #3 #87cefa98 models
> color #3 #87cefaa7 models
> color #3 #87cefa99 models
> color #3 #87cefaa4 models
> color #3 #87cefaa3 models
> volume #3 level 0.35
> fitmap #26 inMap #3
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) using 10075 atoms
average map value = 0.2438, steps = 52
shifted from previous position = 0.293
rotated from previous position = 0.36 degrees
atoms outside contour = 7077, contour level = 0.35
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.84462737 0.15456521 -0.51255653 282.60576624
0.06681694 0.91949322 0.38738573 335.32756599
0.53116861 -0.36144406 0.76630157 241.89923621
Axis -0.58158875 -0.81062320 -0.06815088
Axis point -335.92841792 0.00000000 139.55904352
Rotation angle (degrees) 40.07422511
Shift along axis -452.67028623
> volume #3 level 0.34
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_sharp_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> ui tool show "Side View"
> rock y 20 136
[Repeated 1 time(s)]
> volume #3 level 0.32
> volume #3 level 0.33
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
> hide #!3 models
> show #!50 models
> volume #50 level 5
> volume #50 level 4.6
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
No frames have been recorded
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
> fitmap #26 inMap #50
Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
J842_005_volume_map_EMReady.mrc (#50) using 10075 atoms
average map value = 2.525, steps = 52
shifted from previous position = 0.107
rotated from previous position = 0.359 degrees
atoms outside contour = 7517, contour level = 4.6
Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:
Matrix rotation and translation
0.84685173 0.15716115 -0.50807727 282.58642125
0.06188411 0.91973007 0.38764280 335.21799844
0.52821633 -0.35971789 0.76914923 241.85487927
Axis -0.58331859 -0.80883211 -0.07436418
Axis point -334.58664400 0.00000000 135.85619956
Rotation angle (degrees) 39.83740038
Shift along axis -453.95833613
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_EMReady_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
> select add #26
10075 atoms, 10266 bonds, 1253 residues, 1 model selected
> cartoon hide sel
> show sel target ab
> style sel ball
Changed 10075 atom styles
> color sel byhetero
> select clear
> cartoon #26,50
> hide #26,50 target a
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #26 models
> show #26 models
> hide #!50 models
> show #!11 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> show #!7 models
> hide #!11 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
2 models selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel light sea green
[Repeated 1 time(s)]
> color #7 #b2ffff9d models
> color #7 #b2ffffd9 models
> color #7 #b2ffffb7 models
> color #7 #b2ffffa7 models
> color #7 #b2ffffa6 models
> select clear
> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true
> volume #7 level 0.22
> volume #7 level 0.2
> volume #7 level 0.18
> volume #7 level 0.16
> volume #7 level 0.18
> volume #7 level 0.2
> volume #7 level 0.18
> rock y 20 136
> movie record supersample 3 size 1800, 2000
> rock y 20 136
> wait
> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
\u2014\u2014\u2014 End of log from Mon Oct 7 10:20:32 2024 \u2014\u2014\u2014
opened ChimeraX session
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 11 days, 12 hours, 23 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2415:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 7MT016923MAL
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Note:
See TracTickets
for help on using tickets.
